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 (
    10320, 10321, 10322, 9690, 10106, 10105, 
    10104, 10103, 10206, 10209, 10216, 
    10203, 10204, 10205, 10207, 10208, 
    10210, 10211, 10212, 10213, 10214, 
    10215, 10217, 10218, 10219, 10220, 
    10221, 10222, 10323, 10324, 10325, 
    10326
  ) 
  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 0.00599

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 (10320,10321,10322,9690,10106,10105,10104,10103,10206,10209,10216,10203,10204,10205,10207,10208,10210,10211,10212,10213,10214,10215,10217,10218,10219,10220,10221,10222,10323,10324,10325,10326)",
      "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
    }
  }
}

Result

product_id price
9690 4000.00000000
10103 4702.31000000
10104 4702.31000000
10105 4702.31000000
10106 4702.31000000
10203 1894.30000000
10204 1894.30000000
10205 1894.30000000
10206 1894.30000000
10207 1894.30000000
10208 1894.30000000
10209 1894.30000000
10210 1894.30000000
10211 1894.30000000
10212 1894.30000000
10213 1894.30000000
10214 1894.30000000
10215 1894.30000000
10216 1894.30000000
10217 1894.30000000
10218 1894.30000000
10219 1894.30000000
10220 1894.30000000
10221 1894.30000000
10222 1894.30000000
10320 2930.59000000
10321 2930.59000000
10322 2930.59000000
10323 518.70000000
10324 518.70000000
10325 518.70000000
10326 518.70000000