SELECT 
  cscart_product_prices.product_id, 
  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 
WHERE 
  cscart_product_prices.product_id IN (
    12969, 10144, 10145, 10146, 10147, 10148, 
    10149, 10150, 10151, 10152, 10293, 
    10294, 10295, 10724, 10725, 10343, 
    10345, 10346, 10347, 10348, 10349, 
    10350, 10351, 10352, 10353, 10354, 
    10355, 10356, 10357, 10358, 10359, 
    10360
  ) 
  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 0.00064

JSON explain

{
  "query_block": {
    "select_id": 1,
    "table": {
      "table_name": "cscart_product_prices",
      "access_type": "range",
      "possible_keys": ["usergroup", "product_id", "lower_limit", "usergroup_id"],
      "key": "product_id",
      "key_length": "3",
      "used_key_parts": ["product_id"],
      "rows": 32,
      "filtered": 99.23484039,
      "index_condition": "cscart_product_prices.product_id in (12969,10144,10145,10146,10147,10148,10149,10150,10151,10152,10293,10294,10295,10724,10725,10343,10345,10346,10347,10348,10349,10350,10351,10352,10353,10354,10355,10356,10357,10358,10359,10360)",
      "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
    }
  }
}

Result

product_id price
10144 1606.00000000
10145 1606.00000000
10146 1606.00000000
10147 1606.00000000
10148 1606.00000000
10149 1606.00000000
10150 1606.00000000
10151 1606.00000000
10152 1606.00000000
10293 2206.30000000
10294 2206.30000000
10295 2206.30000000
10343 2121.60000000
10345 2121.60000000
10346 2121.60000000
10347 2121.60000000
10348 2121.60000000
10349 2121.60000000
10350 2121.60000000
10351 2121.60000000
10352 2121.60000000
10353 2121.60000000
10354 2121.60000000
10355 2121.60000000
10356 2121.60000000
10357 2121.60000000
10358 2121.60000000
10359 2121.60000000
10360 2121.60000000
10724 2206.30000000
10725 2206.30000000
12969 1606.00000000