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 (
    10343, 10345, 10346, 10347, 10348, 10349, 
    10350, 10351, 10352, 10353, 10354, 
    10355, 10356, 10357, 10358, 10359, 
    10360, 10361, 10362, 10363, 10364, 
    10365, 10366, 10367, 10368, 12671, 
    12672, 15779, 12673, 12674, 12675, 
    12676
  ) 
  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 0.00062

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 (10343,10345,10346,10347,10348,10349,10350,10351,10352,10353,10354,10355,10356,10357,10358,10359,10360,10361,10362,10363,10364,10365,10366,10367,10368,12671,12672,15779,12673,12674,12675,12676)",
      "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
    }
  }
}

Result

product_id price
10343 2121.60000000
10345 2121.60000000
10346 2121.60000000
10347 2121.60000000
10348 2121.60000000
10349 2121.60000000
10350 2121.60000000
10351 2121.60000000
10352 2121.60000000
10353 2121.60000000
10354 2121.60000000
10355 2121.60000000
10356 2121.60000000
10357 2121.60000000
10358 2121.60000000
10359 2121.60000000
10360 2121.60000000
10361 2121.60000000
10362 2121.60000000
10363 2121.60000000
10364 2121.60000000
10365 2121.60000000
10366 2121.60000000
10367 2121.60000000
10368 2121.60000000
12671 921.36000000
12672 921.36000000
12673 921.36000000
12674 921.36000000
12675 921.36000000
12676 921.36000000
15779 921.36000000