SELECT 
  products.company_id, 
  COUNT(DISTINCT products.product_id) as products_count 
FROM 
  ushop_products as products 
  LEFT JOIN ushop_product_descriptions as descr1 ON descr1.product_id = products.product_id 
  AND descr1.lang_code = 'es' 
  LEFT JOIN ushop_product_prices as prices ON prices.product_id = products.product_id 
  AND prices.lower_limit = 1 
  LEFT JOIN ushop_companies AS companies ON companies.company_id = products.company_id 
  INNER JOIN ushop_products_categories as products_categories ON products_categories.product_id = products.product_id 
  INNER JOIN ushop_categories ON ushop_categories.category_id = products_categories.category_id 
  AND (
    ushop_categories.usergroup_ids = '' 
    OR FIND_IN_SET(
      0, ushop_categories.usergroup_ids
    ) 
    OR FIND_IN_SET(
      1, ushop_categories.usergroup_ids
    )
  ) 
  AND ushop_categories.status IN ('A', 'H') 
  AND ushop_categories.storefront_id IN (0, 1) 
  LEFT JOIN ushop_cp_auctions as auctions ON products.product_id = auctions.product_id 
  LEFT JOIN ushop_users ON products.company_id = ushop_users.company_id 
  AND ushop_users.user_type = 'V' 
  AND ushop_users.user_id = 0 
  LEFT JOIN ushop_product_popularity as popularity ON popularity.product_id = products.product_id 
WHERE 
  1 = 1 
  AND companies.status IN ('A') 
  AND products.status IN ('A') 
  AND (
    products.usergroup_ids = '' 
    OR FIND_IN_SET(0, products.usergroup_ids) 
    OR FIND_IN_SET(1, products.usergroup_ids)
  ) 
  AND products.status IN ('A') 
  AND prices.usergroup_id IN (0, 0, 1) 
  AND products.parent_product_id = 0 
  AND (
    CASE WHEN (
      products.cp_active_auction_id > 0
    ) THEN (
      (
        auctions.users = '' 
        OR FIND_IN_SET(0, auctions.users)
      ) 
      AND auctions.show_on_category = 'Y'
    ) ELSE 1 END 
    OR ushop_users.company_id = products.company_id
  ) 
  AND products.product_type <> 'W' 
  AND products.product_type != 'D' 
  AND products.company_id IN (2) 
GROUP BY 
  products.company_id

Query time 0.00235

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "61.72"
    },
    "grouping_operation": {
      "using_filesort": false,
      "nested_loop": [
        {
          "table": {
            "table_name": "companies",
            "access_type": "const",
            "possible_keys": [
              "PRIMARY"
            ],
            "key": "PRIMARY",
            "used_key_parts": [
              "company_id"
            ],
            "key_length": "4",
            "ref": [
              "const"
            ],
            "rows_examined_per_scan": 1,
            "rows_produced_per_join": 1,
            "filtered": "100.00",
            "cost_info": {
              "read_cost": "0.00",
              "eval_cost": "0.10",
              "prefix_cost": "0.00",
              "data_read_per_join": "6K"
            },
            "used_columns": [
              "company_id",
              "status"
            ]
          }
        },
        {
          "table": {
            "table_name": "products",
            "access_type": "ALL",
            "possible_keys": [
              "PRIMARY",
              "status",
              "idx_parent_product_id"
            ],
            "rows_examined_per_scan": 266,
            "rows_produced_per_join": 21,
            "filtered": "7.92",
            "cost_info": {
              "read_cost": "29.44",
              "eval_cost": "2.11",
              "prefix_cost": "31.55",
              "data_read_per_join": "90K"
            },
            "used_columns": [
              "product_id",
              "product_type",
              "status",
              "company_id",
              "usergroup_ids",
              "parent_product_id",
              "cp_active_auction_id"
            ],
            "attached_condition": "((`marketplace`.`products`.`company_id` = 2) and (`marketplace`.`products`.`parent_product_id` = 0) and (`marketplace`.`products`.`status` = 'A') and ((`marketplace`.`products`.`usergroup_ids` = '') or (0 <> find_in_set(0,`marketplace`.`products`.`usergroup_ids`)) or (0 <> find_in_set(1,`marketplace`.`products`.`usergroup_ids`))) and (`marketplace`.`products`.`product_type` <> 'W') and (`marketplace`.`products`.`product_type` <> 'D'))"
          }
        },
        {
          "table": {
            "table_name": "auctions",
            "access_type": "ref",
            "possible_keys": [
              "product_id"
            ],
            "key": "product_id",
            "used_key_parts": [
              "product_id"
            ],
            "key_length": "4",
            "ref": [
              "marketplace.products.product_id"
            ],
            "rows_examined_per_scan": 1,
            "rows_produced_per_join": 21,
            "filtered": "100.00",
            "index_condition": "<if>(is_not_null_compl(auctions), (`marketplace`.`products`.`product_id` = `marketplace`.`auctions`.`product_id`), true)",
            "cost_info": {
              "read_cost": "5.27",
              "eval_cost": "2.11",
              "prefix_cost": "38.92",
              "data_read_per_join": "4K"
            },
            "used_columns": [
              "product_id",
              "users",
              "show_on_category"
            ]
          }
        },
        {
          "table": {
            "table_name": "prices",
            "access_type": "ref",
            "possible_keys": [
              "usergroup",
              "product_id",
              "lower_limit",
              "usergroup_id"
            ],
            "key": "usergroup",
            "used_key_parts": [
              "product_id"
            ],
            "key_length": "3",
            "ref": [
              "marketplace.products.product_id"
            ],
            "rows_examined_per_scan": 1,
            "rows_produced_per_join": 20,
            "filtered": "98.88",
            "using_index": true,
            "cost_info": {
              "read_cost": "5.27",
              "eval_cost": "2.08",
              "prefix_cost": "46.29",
              "data_read_per_join": "499"
            },
            "used_columns": [
              "product_id",
              "lower_limit",
              "usergroup_id"
            ],
            "attached_condition": "((`marketplace`.`prices`.`lower_limit` = 1) and (`marketplace`.`prices`.`usergroup_id` in (0,0,1)))"
          }
        },
        {
          "table": {
            "table_name": "products_categories",
            "access_type": "ref",
            "possible_keys": [
              "PRIMARY",
              "pt"
            ],
            "key": "pt",
            "used_key_parts": [
              "product_id"
            ],
            "key_length": "3",
            "ref": [
              "marketplace.products.product_id"
            ],
            "rows_examined_per_scan": 1,
            "rows_produced_per_join": 20,
            "filtered": "100.00",
            "cost_info": {
              "read_cost": "5.21",
              "eval_cost": "2.08",
              "prefix_cost": "53.58",
              "data_read_per_join": "333"
            },
            "used_columns": [
              "product_id",
              "category_id"
            ]
          }
        },
        {
          "table": {
            "table_name": "ushop_categories",
            "access_type": "eq_ref",
            "possible_keys": [
              "PRIMARY",
              "c_status",
              "p_category_id"
            ],
            "key": "PRIMARY",
            "used_key_parts": [
              "category_id"
            ],
            "key_length": "3",
            "ref": [
              "marketplace.products_categories.category_id"
            ],
            "rows_examined_per_scan": 1,
            "rows_produced_per_join": 1,
            "filtered": "5.00",
            "cost_info": {
              "read_cost": "5.21",
              "eval_cost": "0.10",
              "prefix_cost": "60.87",
              "data_read_per_join": "3K"
            },
            "used_columns": [
              "category_id",
              "storefront_id",
              "usergroup_ids",
              "status"
            ],
            "attached_condition": "(((`marketplace`.`ushop_categories`.`usergroup_ids` = '') or (0 <> find_in_set(0,`marketplace`.`ushop_categories`.`usergroup_ids`)) or (0 <> find_in_set(1,`marketplace`.`ushop_categories`.`usergroup_ids`))) and (`marketplace`.`ushop_categories`.`status` in ('A','H')) and (`marketplace`.`ushop_categories`.`storefront_id` in (0,1)))"
          }
        },
        {
          "table": {
            "table_name": "ushop_users",
            "access_type": "const",
            "possible_keys": [
              "PRIMARY"
            ],
            "key": "PRIMARY",
            "used_key_parts": [
              "user_id"
            ],
            "key_length": "3",
            "ref": [
              "const"
            ],
            "rows_examined_per_scan": 1,
            "rows_produced_per_join": 1,
            "filtered": "100.00",
            "cost_info": {
              "read_cost": "0.01",
              "eval_cost": "0.10",
              "prefix_cost": "60.99",
              "data_read_per_join": "6K"
            },
            "used_columns": [
              "user_id",
              "user_type",
              "company_id"
            ],
            "attached_condition": "(<if>(found_match(ushop_users), ((0 <> (case when (`marketplace`.`products`.`cp_active_auction_id` > 0) then (((`marketplace`.`auctions`.`users` = '') or (0 <> find_in_set(0,`marketplace`.`auctions`.`users`))) and (`marketplace`.`auctions`.`show_on_category` = 'Y')) else 1 end)) or (`marketplace`.`ushop_users`.`company_id` = 2)), true) and <if>(is_not_null_compl(ushop_users), ((`marketplace`.`ushop_users`.`company_id` = 2) and (`marketplace`.`ushop_users`.`user_type` = 'V')), true))"
          }
        },
        {
          "table": {
            "table_name": "popularity",
            "access_type": "eq_ref",
            "possible_keys": [
              "PRIMARY",
              "total"
            ],
            "key": "PRIMARY",
            "used_key_parts": [
              "product_id"
            ],
            "key_length": "3",
            "ref": [
              "marketplace.products.product_id"
            ],
            "rows_examined_per_scan": 1,
            "rows_produced_per_join": 1,
            "filtered": "100.00",
            "using_index": true,
            "cost_info": {
              "read_cost": "0.26",
              "eval_cost": "0.10",
              "prefix_cost": "61.35",
              "data_read_per_join": "33"
            },
            "used_columns": [
              "product_id"
            ]
          }
        },
        {
          "table": {
            "table_name": "descr1",
            "access_type": "eq_ref",
            "possible_keys": [
              "PRIMARY",
              "product_id"
            ],
            "key": "PRIMARY",
            "used_key_parts": [
              "product_id",
              "lang_code"
            ],
            "key_length": "9",
            "ref": [
              "marketplace.products.product_id",
              "const"
            ],
            "rows_examined_per_scan": 1,
            "rows_produced_per_join": 1,
            "filtered": "100.00",
            "using_index": true,
            "cost_info": {
              "read_cost": "0.26",
              "eval_cost": "0.10",
              "prefix_cost": "61.72",
              "data_read_per_join": "6K"
            },
            "used_columns": [
              "product_id",
              "lang_code"
            ]
          }
        }
      ]
    }
  }
}

Result

company_id products_count
2 3