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 (
    10414, 10415, 10416, 12856, 10417, 10418, 
    10419, 10420, 10421, 10422, 10423, 
    10424, 10384, 10383, 10382, 10753, 
    10754, 10755, 10296, 10297, 10298, 
    10299, 10300, 10446, 10756, 10757, 
    10758, 13031, 13032, 13033, 13034, 
    13035
  ) 
  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 0.00079

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 (10414,10415,10416,12856,10417,10418,10419,10420,10421,10422,10423,10424,10384,10383,10382,10753,10754,10755,10296,10297,10298,10299,10300,10446,10756,10757,10758,13031,13032,13033,13034,13035)",
      "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
    }
  }
}

Result

product_id price
10296 3409.73000000
10297 3409.73000000
10298 3409.73000000
10299 3409.73000000
10300 3409.73000000
10382 4944.00000000
10383 4944.00000000
10384 4944.00000000
10414 1317.94000000
10415 1317.94000000
10416 1317.94000000
10417 1317.94000000
10418 1317.94000000
10419 1317.94000000
10420 1317.94000000
10421 1317.94000000
10422 1317.94000000
10423 1317.94000000
10424 1317.94000000
10446 3409.73000000
10753 7644.03000000
10754 7644.03000000
10755 7644.03000000
10756 7644.03000000
10757 7644.03000000
10758 7644.03000000
12856 1317.94000000
13031 2106.01000000
13032 2106.01000000
13033 2106.01000000
13034 2106.01000000
13035 2106.01000000