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 (
    94587, 94054, 94053, 94006, 94509, 94508, 
    94481, 94479, 94478, 94265, 94269, 
    98604, 93778, 93573, 94107, 94003, 
    93779, 93367, 93366, 93365
  ) 
  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 0.00050

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
93365 1.69000000
93366 1.69000000
93367 1.69000000
93573 1.69000000
93778 1.69000000
93779 1.69000000
94003 1.69000000
94006 1.69000000
94053 1.69000000
94054 1.69000000
94107 1.69000000
94265 1.69000000
94269 1.69000000
94478 1.69000000
94479 1.69000000
94481 1.69000000
94508 1.69000000
94509 1.69000000
94587 1.69000000
98604 1.69000000