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 (
    6509, 6508, 32956, 19632, 61415, 68414, 
    30699, 68403, 68436, 69379, 30700, 
    30704
  ) 
  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 0.06267

JSON explain

{
  "query_block": {
    "select_id": 1,
    "filesort": {
      "sort_key": "cscart_product_prices.product_id",
      "temporary_table": {
        "table": {
          "table_name": "cscart_product_prices",
          "access_type": "ref",
          "possible_keys": [
            "usergroup",
            "product_id",
            "lower_limit",
            "usergroup_id"
          ],
          "key": "lower_limit",
          "key_length": "3",
          "used_key_parts": ["lower_limit"],
          "ref": ["const"],
          "rows": 66983,
          "filtered": 0.426326841,
          "attached_condition": "cscart_product_prices.lower_limit <=> 1 and cscart_product_prices.product_id in (6509,6508,32956,19632,61415,68414,30699,68403,68436,69379,30700,30704) and cscart_product_prices.usergroup_id in (0,1)"
        }
      }
    }
  }
}