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 (
    10469, 10468, 10467, 10466, 12582, 12583, 
    12584, 10465, 10464, 10463, 10462, 
    10461, 10460, 10459, 12581, 12699, 
    12698, 12697, 12696, 12695, 12694, 
    12693, 12692, 12691, 10447, 10448, 
    10449, 10450, 10451, 10452, 10453, 
    10454
  ) 
  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 0.01109

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 (10469,10468,10467,10466,12582,12583,12584,10465,10464,10463,10462,10461,10460,10459,12581,12699,12698,12697,12696,12695,12694,12693,12692,12691,10447,10448,10449,10450,10451,10452,10453,10454)",
      "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
    }
  }
}

Result

product_id price
10447 1894.30000000
10448 1894.30000000
10449 1894.30000000
10450 1894.30000000
10451 1894.30000000
10452 1894.30000000
10453 1894.30000000
10454 1894.30000000
10459 1708.80000000
10460 1708.80000000
10461 1708.80000000
10462 1708.80000000
10463 1708.80000000
10464 1708.80000000
10465 1708.80000000
10466 1036.29000000
10467 1036.29000000
10468 1036.29000000
10469 1036.29000000
12581 70507.12000000
12582 41728.72000000
12583 41728.72000000
12584 41160.00000000
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