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 (
    41341, 41340, 47922, 47921, 41343, 47896, 
    47924, 47923, 41339, 35829, 2085, 35792, 
    637, 31872, 35855, 33606, 47895, 47280, 
    48032, 48322, 48033, 48037, 48031, 
    48034, 48036, 48035, 47095, 48323, 
    47096, 48324, 47092, 47094
  ) 
  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 0.00324

JSON explain

{
  "query_block": {
    "select_id": 1,
    "nested_loop": [
      {
        "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": 99.9960556,
          "index_condition": "cscart_product_prices.product_id in (41341,41340,47922,47921,41343,47896,47924,47923,41339,35829,2085,35792,637,31872,35855,33606,47895,47280,48032,48322,48033,48037,48031,48034,48036,48035,47095,48323,47096,48324,47092,47094)",
          "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
        }
      }
    ]
  }
}