SELECT 
  IF(
    `C`.`address` IS NULL, 'Не определено', 
    `C`.`address`
  ) AS `address`, 
  `S`.`is_basic`, 
  `PS`.`count`, 
  `PS`.`price`, 
  `S`.`stock_id`, 
  `S`.`fias_id` 
FROM 
  `cscart_company_stocks` AS `S` 
  JOIN `cscart_products` AS `P` ON `P`.`company_id` = `S`.`company_id` 
  JOIN `cscart_product_stocks` AS `PS` ON `S`.`stock_id` = `PS`.`stock_id` 
  AND `PS`.`product_id` = `P`.`product_id` 
  LEFT JOIN `cscart_custom_city` AS `C` ON `C`.`fias_id` = `S`.`fias_id` 
WHERE 
  `P`.`product_id` = 29040 
GROUP BY 
  `S`.`stock_id`, 
  `PS`.`position` 
ORDER BY 
  `PS`.`position`

Query time 0.00059

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "0.92"
    },
    "ordering_operation": {
      "using_filesort": true,
      "grouping_operation": {
        "using_temporary_table": true,
        "using_filesort": false,
        "nested_loop": [
          {
            "table": {
              "table_name": "P",
              "access_type": "const",
              "possible_keys": [
                "PRIMARY",
                "cscart_products_product_id_index"
              ],
              "key": "PRIMARY",
              "used_key_parts": [
                "product_id"
              ],
              "key_length": "3",
              "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": "7K"
              },
              "used_columns": [
                "product_id",
                "company_id"
              ]
            }
          },
          {
            "table": {
              "table_name": "PS",
              "access_type": "ref",
              "possible_keys": [
                "cscart_product_stocks_pk",
                "product_stocks_company_stocks__fk"
              ],
              "key": "cscart_product_stocks_pk",
              "used_key_parts": [
                "product_id"
              ],
              "key_length": "4",
              "ref": [
                "const"
              ],
              "rows_examined_per_scan": 1,
              "rows_produced_per_join": 1,
              "filtered": "100.00",
              "cost_info": {
                "read_cost": "0.44",
                "eval_cost": "0.10",
                "prefix_cost": "0.54",
                "data_read_per_join": "24"
              },
              "used_columns": [
                "product_id",
                "stock_id",
                "count",
                "price",
                "position"
              ]
            }
          },
          {
            "table": {
              "table_name": "S",
              "access_type": "eq_ref",
              "possible_keys": [
                "PRIMARY"
              ],
              "key": "PRIMARY",
              "used_key_parts": [
                "stock_id"
              ],
              "key_length": "4",
              "ref": [
                "dev2.PS.stock_id"
              ],
              "rows_examined_per_scan": 1,
              "rows_produced_per_join": 0,
              "filtered": "10.00",
              "cost_info": {
                "read_cost": "0.25",
                "eval_cost": "0.01",
                "prefix_cost": "0.89",
                "data_read_per_join": "40"
              },
              "used_columns": [
                "stock_id",
                "company_id",
                "fias_id",
                "is_basic"
              ],
              "attached_condition": "('696' = `dev2`.`S`.`company_id`)"
            }
          },
          {
            "table": {
              "table_name": "C",
              "access_type": "ref",
              "possible_keys": [
                "idx_custom_city_fias_id"
              ],
              "key": "idx_custom_city_fias_id",
              "used_key_parts": [
                "fias_id"
              ],
              "key_length": "386",
              "ref": [
                "dev2.S.fias_id"
              ],
              "rows_examined_per_scan": 1,
              "rows_produced_per_join": 0,
              "filtered": "100.00",
              "cost_info": {
                "read_cost": "0.03",
                "eval_cost": "0.01",
                "prefix_cost": "0.92",
                "data_read_per_join": "543"
              },
              "used_columns": [
                "city_id",
                "address",
                "fias_id"
              ]
            }
          }
        ]
      }
    }
  }
}