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 (
    10610, 10611, 10612, 10613, 10614, 10615, 
    10616, 10617, 10618, 10619, 10620, 
    10621, 10622, 10623, 10624, 9685, 10653, 
    10646, 10645, 10647, 10648, 10649, 
    10726, 10650, 10547, 9789, 10655, 10654, 
    10605, 10604, 9873, 9972
  ) 
  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 0.00075

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 (10610,10611,10612,10613,10614,10615,10616,10617,10618,10619,10620,10621,10622,10623,10624,9685,10653,10646,10645,10647,10648,10649,10726,10650,10547,9789,10655,10654,10605,10604,9873,9972)",
      "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
    }
  }
}

Result

product_id price
9685 4000.00000000
9789 1381.72000000
9873 2997.44000000
9972 582.40000000
10547 1381.72000000
10604 2997.44000000
10605 2997.44000000
10610 1292.58000000
10611 1292.58000000
10612 1292.58000000
10613 1292.58000000
10614 1292.58000000
10615 1292.58000000
10616 1292.58000000
10617 1292.58000000
10618 1292.58000000
10619 1292.58000000
10620 1292.58000000
10621 1292.58000000
10622 1292.58000000
10623 1292.58000000
10624 1292.58000000
10645 1381.72000000
10646 1381.72000000
10647 1381.72000000
10648 1381.72000000
10649 1381.72000000
10650 1381.72000000
10653 1381.72000000
10654 2997.44000000
10655 2997.44000000
10726 1381.72000000