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 (
    10031, 10032, 10033, 10034, 10035, 10036, 
    10037, 10038, 10039, 10040, 10756, 
    10757, 10758, 10397, 10398, 10399, 
    10400, 10401, 10402, 12700, 12546, 
    12633, 12573, 12548, 12580, 12576, 
    12565, 12567, 12549, 12581, 12557, 
    12558
  ) 
  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 0.00068

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 (10031,10032,10033,10034,10035,10036,10037,10038,10039,10040,10756,10757,10758,10397,10398,10399,10400,10401,10402,12700,12546,12633,12573,12548,12580,12576,12565,12567,12549,12581,12557,12558)",
      "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
    }
  }
}

Result

product_id price
10031 1716.01000000
10032 1716.01000000
10033 1716.01000000
10034 1716.01000000
10035 1716.01000000
10036 1716.01000000
10037 1716.01000000
10038 1716.01000000
10039 1716.01000000
10040 1716.01000000
10397 1326.01000000
10398 1326.01000000
10399 1326.01000000
10400 1326.01000000
10401 1326.01000000
10402 1326.01000000
10756 7644.03000000
10757 7644.03000000
10758 7644.03000000
12546 67629.15000000
12548 52280.84000000
12549 43647.16000000
12557 52280.84000000
12558 82018.56000000
12565 67629.15000000
12567 10552.12000000
12573 68108.92000000
12576 41728.72000000
12580 11031.68000000
12581 70507.12000000
12633 67629.15000000
12700 1326.01000000