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 (
    1233, 1234, 1232, 1231, 1222, 105, 71, 
    104, 72, 34, 36, 1175, 1911, 1245, 99, 
    1311, 78, 100, 98, 88, 1319, 85, 1280, 
    1279, 283, 1247, 1110, 985, 1300, 1035, 
    1028, 603, 1268, 1269, 1392, 1380, 1391, 
    1388, 968, 1163, 84, 38, 1162, 1299, 
    1350, 1314, 154, 1328
  ) 
  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 0.00189

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": 48,
      "filtered": 9.795915604,
      "index_condition": "cscart_product_prices.product_id in (1233,1234,1232,1231,1222,105,71,104,72,34,36,1175,1911,1245,99,1311,78,100,98,88,1319,85,1280,1279,283,1247,1110,985,1300,1035,1028,603,1268,1269,1392,1380,1391,1388,968,1163,84,38,1162,1299,1350,1314,154,1328)",
      "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
    }
  }
}

Result

product_id price
34 44000.00000000
36 110000.00000000
38 21000.00000000
71 0.00000000
72 0.00000000
78 20000.00000000
84 21000.00000000
85 30000.00000000
88 76000.00000000
98 0.00000000
99 21500.00000000
100 20000.00000000
104 0.00000000
105 0.00000000
154 103636.00000000
283 70000.00000000
603 0.00000000
968 0.00000000
985 40800.00000000
1028 30000.00000000
1035 0.00000000
1110 0.00000000
1162 21000.00000000
1163 24600.00000000
1175 70200.00000000
1222 54000.00000000
1231 96000.00000000
1232 96000.00000000
1233 96000.00000000
1234 96000.00000000
1245 0.00000000
1247 0.00000000
1268 44000.00000000
1269 38000.00000000
1279 32000.00000000
1280 0.00000000
1299 48000.00000000
1300 32000.00000000
1311 18000.00000000
1314 32000.00000000
1319 180000.00000000
1328 12000.00000000
1350 0.00000000
1380 33000.00000000
1388 45000.00000000
1391 45000.00000000
1392 45000.00000000
1911 52000.00000000