SELECT 
  cscart_product_prices.product_id, 
  COALESCE(
    cscart_master_products_storefront_min_price.price, 
    MIN(
      IF(
        cscart_product_prices.percentage_discount = 0, 
        cscart_product_prices.price, 
        cscart_product_prices.price - (
          cscart_product_prices.price * cscart_product_prices.percentage_discount
        )/ 100
      )
    )
  ) AS price 
FROM 
  cscart_product_prices 
  LEFT JOIN cscart_master_products_storefront_min_price ON cscart_master_products_storefront_min_price.product_id = cscart_product_prices.product_id 
  AND cscart_master_products_storefront_min_price.storefront_id = 1 
WHERE 
  cscart_product_prices.product_id IN (
    66979, 69260, 65085, 65106, 6793, 65116, 
    65110, 65120, 65126, 65127, 65498
  ) 
  AND cscart_product_prices.lower_limit = 1 
  AND cscart_product_prices.usergroup_id IN (0, 1) 
GROUP BY 
  cscart_product_prices.product_id

Query time 0.00163

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "2.52"
    },
    "grouping_operation": {
      "using_filesort": false,
      "nested_loop": [
        {
          "table": {
            "table_name": "cscart_master_products_storefront_min_price",
            "access_type": "system",
            "possible_keys": [
              "PRIMARY"
            ],
            "rows_examined_per_scan": 0,
            "rows_produced_per_join": 1,
            "filtered": "0.00",
            "const_row_not_found": true,
            "cost_info": {
              "read_cost": "0.00",
              "eval_cost": "0.10",
              "prefix_cost": "0.00",
              "data_read_per_join": "16"
            },
            "used_columns": [
              "storefront_id",
              "product_id",
              "price"
            ]
          }
        },
        {
          "table": {
            "table_name": "cscart_product_prices",
            "access_type": "range",
            "possible_keys": [
              "usergroup",
              "product_id",
              "lower_limit",
              "usergroup_id",
              "idx_product_prices_usergroup_limit",
              "idx_prices_discount_lookup",
              "idx_prices_min_calc",
              "idx_prices_usergroup_lookup",
              "idx_prices_usergroup_product"
            ],
            "key": "idx_prices_discount_lookup",
            "used_key_parts": [
              "product_id",
              "lower_limit"
            ],
            "key_length": "6",
            "rows_examined_per_scan": 11,
            "rows_produced_per_join": 2,
            "filtered": "20.00",
            "using_index": true,
            "cost_info": {
              "read_cost": "2.30",
              "eval_cost": "0.22",
              "prefix_cost": "2.52",
              "data_read_per_join": "52"
            },
            "used_columns": [
              "product_id",
              "price",
              "percentage_discount",
              "lower_limit",
              "usergroup_id"
            ],
            "attached_condition": "((`cscart_db`.`cscart_product_prices`.`lower_limit` = 1) and (`cscart_db`.`cscart_product_prices`.`product_id` in (66979,69260,65085,65106,6793,65116,65110,65120,65126,65127,65498)) and (`cscart_db`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
          }
        }
      ]
    }
  }
}