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 (
    10462, 10463, 10464, 10465, 10625, 10626, 
    10627, 10628, 10629, 10630, 10631, 
    10632, 10633, 10634, 10635, 10636, 
    12944, 10829, 10830, 10831, 10832, 
    10833, 10834, 10835, 10836, 10837, 
    10838, 10839, 12985, 12986, 12987, 
    12988
  ) 
  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 0.00049

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 (10462,10463,10464,10465,10625,10626,10627,10628,10629,10630,10631,10632,10633,10634,10635,10636,12944,10829,10830,10831,10832,10833,10834,10835,10836,10837,10838,10839,12985,12986,12987,12988)",
      "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
    }
  }
}

Result

product_id price
10462 1708.80000000
10463 1708.80000000
10464 1708.80000000
10465 1708.80000000
10625 1582.30000000
10626 1582.30000000
10627 1582.30000000
10628 1582.30000000
10629 1582.30000000
10630 1582.30000000
10631 1582.30000000
10632 1582.30000000
10633 1582.30000000
10634 1582.30000000
10635 1582.30000000
10636 1582.30000000
10829 3053.16000000
10830 3053.16000000
10831 3053.16000000
10832 3053.16000000
10833 3053.16000000
10834 3053.16000000
10835 3053.16000000
10836 3053.16000000
10837 3053.16000000
10838 3053.16000000
10839 3053.16000000
12944 1560.00000000
12985 921.36000000
12986 921.36000000
12987 921.36000000
12988 921.36000000