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 (
    9804, 9809, 9810, 9811, 9812, 9807, 9808, 
    9683, 10455, 10456, 10454, 10453, 10452, 
    10451, 10450, 10449, 10448, 10447, 
    12691, 12692, 12693, 12694, 12695, 
    12696, 12697, 12698, 12699, 10370, 
    10372, 10374, 10376, 10377, 10378, 
    10379, 10380, 10381, 10371, 10373, 
    10375, 10387, 10395, 10390, 10394, 
    10393, 10392, 10386, 10389, 10388, 
    10637, 10638, 10639, 10640, 10641, 
    10744, 10745, 10746, 9905, 10168, 10041, 
    10643, 10606, 10094, 10097, 12703
  ) 
  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 0.00120

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 (9804,9809,9810,9811,9812,9807,9808,9683,10455,10456,10454,10453,10452,10451,10450,10449,10448,10447,12691,12692,12693,12694,12695,12696,12697,12698,12699,10370,10372,10374,10376,10377,10378,10379,10380,10381,10371,10373,10375,10387,10395,10390,10394,10393,10392,10386,10389,10388,10637,10638,10639,10640,10641,10744,10745,10746,9905,10168,10041,10643,10606,10094,10097,12703)",
      "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
    }
  }
}

Result

product_id price
9683 4000.00000000
9804 1292.58000000
9807 1292.58000000
9808 1292.58000000
9809 1292.58000000
9810 1292.58000000
9811 1292.58000000
9812 1292.58000000
9905 1849.73000000
10041 1849.73000000
10094 1849.73000000
10097 1849.73000000
10168 1849.73000000
10370 2763.44000000
10371 2763.44000000
10372 2763.44000000
10373 2763.44000000
10374 2763.44000000
10375 2763.44000000
10376 2763.44000000
10377 2763.44000000
10378 2763.44000000
10379 2763.44000000
10380 2763.44000000
10381 2763.44000000
10386 2540.59000000
10387 2540.59000000
10388 2540.59000000
10389 2540.59000000
10390 2540.59000000
10392 2540.59000000
10393 2540.59000000
10394 2540.59000000
10395 2540.59000000
10447 1894.30000000
10448 1894.30000000
10449 1894.30000000
10450 1894.30000000
10451 1894.30000000
10452 1894.30000000
10453 1894.30000000
10454 1894.30000000
10455 1894.30000000
10456 1894.30000000
10606 1849.73000000
10637 2540.59000000
10638 2540.59000000
10639 2540.59000000
10640 2540.59000000
10641 2540.59000000
10643 1849.73000000
10744 4824.88000000
10745 4824.88000000
10746 4824.88000000
12691 1894.30000000
12692 1894.30000000
12693 1894.30000000
12694 1894.30000000
12695 1894.30000000
12696 1894.30000000
12697 1894.30000000
12698 1894.30000000
12699 1894.30000000
12703 1849.73000000