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 (
    12520, 12497, 12528, 12512, 12511, 12527, 
    10580, 10579, 9936, 9931, 12521, 12504, 
    12502, 12505, 13099, 12514, 12513, 
    9759, 10496, 10560, 10561, 10581, 10102, 
    9940, 10578, 10143, 9947, 10567, 10568, 
    10565, 9933, 12499
  ) 
  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 0.00080

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 (12520,12497,12528,12512,12511,12527,10580,10579,9936,9931,12521,12504,12502,12505,13099,12514,12513,9759,10496,10560,10561,10581,10102,9940,10578,10143,9947,10567,10568,10565,9933,12499)",
      "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
    }
  }
}

Result

product_id price
9759 1955.00000000
9931 1331.00000000
9933 1563.00000000
9936 1331.00000000
9940 2142.00000000
9947 2022.00000000
10102 2142.00000000
10143 2205.00000000
10496 1955.00000000
10560 2098.00000000
10561 2098.00000000
10565 2691.00000000
10567 2691.00000000
10568 2691.00000000
10578 2205.00000000
10579 1791.00000000
10580 1791.00000000
10581 2142.00000000
12497 0.00000000
12499 0.00000000
12502 0.00000000
12504 0.00000000
12505 0.00000000
12511 0.00000000
12512 0.00000000
12513 0.00000000
12514 0.00000000
12520 0.00000000
12521 0.00000000
12527 0.00000000
12528 0.00000000
13099 0.00000000