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 (
    10043, 10042, 10414, 10040, 10030, 10032, 
    10461, 10435, 10442, 10425, 10429, 
    10445
  ) 
  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 0.00046

Explain
id select_type table type possible_keys key key_len ref rows Extra
1 SIMPLE cscart_product_prices range usergroup,product_id,lower_limit,usergroup_id product_id 3 13 Using index condition; Using where

Result

product_id price
10030 41.350000
10032 90.200000
10040 64.590000
10042 67.310000
10043 58.190000
10414 46.310000
10425 94.730000
10429 66.470000
10435 78.720000
10442 63.900000
10445 94.820000
10461 44.300000