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 (
    9878, 9886, 9882, 9888, 10482, 9776, 
    9777, 9781, 9775, 9778, 9779, 9780, 
    9782, 9790, 9787, 9791, 9792, 9795, 
    9784, 9785, 9783, 9786, 9788, 13031, 
    13032, 13033, 13034, 13035, 13036, 
    13037, 13038, 13039
  ) 
  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 0.00058

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 (9878,9886,9882,9888,10482,9776,9777,9781,9775,9778,9779,9780,9782,9790,9787,9791,9792,9795,9784,9785,9783,9786,9788,13031,13032,13033,13034,13035,13036,13037,13038,13039)",
      "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
    }
  }
}

Result

product_id price
9775 1292.58000000
9776 1292.58000000
9777 1292.58000000
9778 1292.58000000
9779 1292.58000000
9780 1292.58000000
9781 1292.58000000
9782 1292.58000000
9783 1292.58000000
9784 1292.58000000
9785 1292.58000000
9786 1292.58000000
9787 1292.58000000
9788 1292.58000000
9790 1292.58000000
9791 1292.58000000
9792 1292.58000000
9795 1292.58000000
9878 1036.29000000
9882 1036.29000000
9886 1036.29000000
9888 1036.29000000
10482 1036.29000000
13031 2106.01000000
13032 2106.01000000
13033 2106.01000000
13034 2106.01000000
13035 2106.01000000
13036 2106.01000000
13037 2106.01000000
13038 2106.01000000
13039 2106.01000000