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 (
    10489, 10471, 9880, 10472, 9885, 10488, 
    9897, 9895, 10467, 9900, 10470, 10466, 
    10477, 9889, 10475, 9890, 10483, 10495, 
    10490, 10469, 9877, 9894, 9891, 10480, 
    9893, 9878, 9886, 9882, 9888, 10482, 
    13091, 12551
  ) 
  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 0.00093

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 (10489,10471,9880,10472,9885,10488,9897,9895,10467,9900,10470,10466,10477,9889,10475,9890,10483,10495,10490,10469,9877,9894,9891,10480,9893,9878,9886,9882,9888,10482,13091,12551)",
      "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
    }
  }
}

Result

product_id price
9877 1036.29000000
9878 1036.29000000
9880 1036.29000000
9882 1036.29000000
9885 1036.29000000
9886 1036.29000000
9888 1036.29000000
9889 1036.29000000
9890 1036.29000000
9891 1036.29000000
9893 1036.29000000
9894 1036.29000000
9895 1036.29000000
9897 1036.29000000
9900 1036.29000000
10466 1036.29000000
10467 1036.29000000
10469 1036.29000000
10470 1036.29000000
10471 1036.29000000
10472 1036.29000000
10475 1036.29000000
10477 1036.29000000
10480 1036.29000000
10482 1036.29000000
10483 1036.29000000
10488 1036.29000000
10489 1036.29000000
10490 1036.29000000
10495 1036.29000000
12551 15215.00000000
13091 6750.00000000