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 (
    90052, 89929, 89312, 89311, 89310, 89309, 
    89985, 89944, 89943, 89402, 89191, 
    89173, 89172, 89551, 89037, 89483, 
    89445, 89443, 88978, 88914
  ) 
  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 0.00081

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 usergroup 9 40 Using where

Result

product_id price
88914 1.69000000
88978 1.69000000
89037 1.69000000
89172 1.69000000
89173 1.69000000
89191 1.69000000
89309 1.69000000
89310 1.69000000
89311 1.69000000
89312 1.69000000
89402 1.69000000
89443 1.69000000
89445 1.69000000
89483 1.69000000
89551 1.69000000
89929 1.69000000
89943 1.69000000
89944 1.69000000
89985 1.69000000
90052 1.69000000