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 (
    65396, 65399, 65457, 65395, 65459, 65482, 
    65387, 65410, 65418, 65388, 65403, 
    65404, 65406, 65407, 65409, 65411, 
    65412, 65413, 65414, 65415, 65417, 
    65433, 65464, 66147, 66183, 64396, 
    65422, 65423, 65426, 65427, 65428, 
    65429, 65430, 65431, 65432, 65434, 
    65435, 65436, 65438, 65439, 65440, 
    65441, 65442, 65443, 65444, 65445, 
    65446, 65447, 65448, 65449, 65450, 
    65451, 65452, 65454, 65455, 65456, 
    65460, 65462, 65465, 65476, 65484, 
    65486, 65487, 65488, 65489, 66133, 
    66134, 66142, 66144, 66145, 66149, 
    66151, 66152, 66153, 66154, 66155, 
    66170, 66179, 66180, 66184
  ) 
  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 0.00664

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "16.34"
    },
    "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": 80,
            "rows_produced_per_join": 16,
            "filtered": "20.00",
            "using_index": true,
            "cost_info": {
              "read_cost": "14.74",
              "eval_cost": "1.60",
              "prefix_cost": "16.34",
              "data_read_per_join": "384"
            },
            "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 (65396,65399,65457,65395,65459,65482,65387,65410,65418,65388,65403,65404,65406,65407,65409,65411,65412,65413,65414,65415,65417,65433,65464,66147,66183,64396,65422,65423,65426,65427,65428,65429,65430,65431,65432,65434,65435,65436,65438,65439,65440,65441,65442,65443,65444,65445,65446,65447,65448,65449,65450,65451,65452,65454,65455,65456,65460,65462,65465,65476,65484,65486,65487,65488,65489,66133,66134,66142,66144,66145,66149,66151,66152,66153,66154,66155,66170,66179,66180,66184)) and (`cscart_db`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
          }
        }
      ]
    }
  }
}