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 (
    10744, 10745, 10746, 10739, 10740, 10741, 
    10742, 10734, 10735, 10736, 10737, 
    10738, 10688, 10727, 10728, 10729, 
    10730, 10731, 10732, 10733, 10713, 
    10714, 10715, 10716, 10717, 10718, 
    10719, 10720, 10721, 10722, 10723, 
    10704
  ) 
  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 0.00065

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 (10744,10745,10746,10739,10740,10741,10742,10734,10735,10736,10737,10738,10688,10727,10728,10729,10730,10731,10732,10733,10713,10714,10715,10716,10717,10718,10719,10720,10721,10722,10723,10704)",
      "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
    }
  }
}

Result

product_id price
10688 3242.59000000
10704 3432.02000000
10713 1537.72000000
10714 1537.72000000
10715 1537.72000000
10716 1537.72000000
10717 1537.72000000
10718 1537.72000000
10719 1537.72000000
10720 1537.72000000
10721 1537.72000000
10722 1537.72000000
10723 1537.72000000
10727 3242.59000000
10728 3242.59000000
10729 3242.59000000
10730 3242.59000000
10731 3242.59000000
10732 3242.59000000
10733 3242.59000000
10734 2294.40000000
10735 2294.40000000
10736 2294.40000000
10737 2294.40000000
10738 2294.40000000
10739 4457.16000000
10740 4457.16000000
10741 4457.16000000
10742 3755.16000000
10744 4824.88000000
10745 4824.88000000
10746 4824.88000000