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 (
    10793, 10794, 10795, 10796, 10797, 10798, 
    10799, 10800, 10801, 10802, 10803, 
    10804, 10805, 10806, 10807, 10808, 
    10809, 10810, 10811, 10812, 10827, 
    10828, 9686, 10767, 10768, 10769, 10770, 
    10771, 10772, 10773, 10774, 10775, 
    10776, 10777, 9689, 10459, 10460, 10461, 
    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
  ) 
  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 0.00110

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": 64,
      "filtered": 99.23484039,
      "index_condition": "cscart_product_prices.product_id in (10793,10794,10795,10796,10797,10798,10799,10800,10801,10802,10803,10804,10805,10806,10807,10808,10809,10810,10811,10812,10827,10828,9686,10767,10768,10769,10770,10771,10772,10773,10774,10775,10776,10777,9689,10459,10460,10461,10462,10463,10464,10465,10625,10626,10627,10628,10629,10630,10631,10632,10633,10634,10635,10636,12944,10829,10830,10831,10832,10833,10834,10835,10836,10837)",
      "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
    }
  }
}

Result

product_id price
9686 4000.00000000
9689 4000.00000000
10459 1708.80000000
10460 1708.80000000
10461 1708.80000000
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
10767 5972.60000000
10768 5972.60000000
10769 5972.60000000
10770 5972.60000000
10771 5972.60000000
10772 5972.60000000
10773 5972.60000000
10774 5972.60000000
10775 5972.60000000
10776 5972.60000000
10777 5972.60000000
10793 1582.30000000
10794 1582.30000000
10795 1582.30000000
10796 1582.30000000
10797 1582.30000000
10798 1582.30000000
10799 1582.30000000
10800 1582.30000000
10801 1582.30000000
10802 1582.30000000
10803 1582.30000000
10804 1582.30000000
10805 1582.30000000
10806 1582.30000000
10807 1582.30000000
10808 1582.30000000
10809 1582.30000000
10810 1582.30000000
10811 1582.30000000
10812 1582.30000000
10827 1582.30000000
10828 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
12944 1560.00000000