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 (
    262440, 264695, 264694, 264697, 339741, 
    339622, 339616, 339574, 339692, 339740, 
    339609, 339737, 339621, 339617, 339620, 
    339587, 339611, 339742, 339710, 339683
  ) 
  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 0.00119

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "56.07"
    },
    "grouping_operation": {
      "using_filesort": false,
      "table": {
        "table_name": "cscart_product_prices",
        "access_type": "range",
        "possible_keys": [
          "usergroup",
          "product_id",
          "lower_limit",
          "usergroup_id"
        ],
        "key": "usergroup",
        "used_key_parts": [
          "product_id",
          "usergroup_id",
          "lower_limit"
        ],
        "key_length": "9",
        "rows_examined_per_scan": 40,
        "rows_produced_per_join": 40,
        "filtered": "100.00",
        "cost_info": {
          "read_cost": "48.07",
          "eval_cost": "8.00",
          "prefix_cost": "56.07",
          "data_read_per_join": "2K"
        },
        "used_columns": [
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "usergroup_id"
        ],
        "attached_condition": "((`webmarco`.`cscart_product_prices`.`lower_limit` = 1) and (`webmarco`.`cscart_product_prices`.`product_id` in (262440,264695,264694,264697,339741,339622,339616,339574,339692,339740,339609,339737,339621,339617,339620,339587,339611,339742,339710,339683)) and (`webmarco`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}

Result

product_id price
262440 0.00000000
264694 0.00000000
264695 0.00000000
264697 0.00000000
339574 45.00000000
339587 85.00000000
339609 12.00000000
339611 65.00000000
339616 45.00000000
339617 55.00000000
339620 30.00000000
339621 160.00000000
339622 60.00000000
339683 26.00000000
339692 4.00000000
339710 40.00000000
339737 68.00000000
339740 94.00000000
339741 27.50000000
339742 98.00000000