SELECT 
  cscart_product_prices.product_id, 
  COALESCE(
    cscart_master_products_storefront_min_price.price, 
    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 
  LEFT JOIN cscart_master_products_storefront_min_price ON cscart_master_products_storefront_min_price.product_id = cscart_product_prices.product_id 
  AND cscart_master_products_storefront_min_price.storefront_id = 1 
WHERE 
  cscart_product_prices.product_id IN (
    3351, 78822, 3316, 3317, 2512, 3326, 
    3327, 3374, 3331, 3335, 3377, 3376, 
    3313, 3368, 3311, 3315, 3314, 3310, 
    3312, 3330, 3332, 3333, 3334, 3336, 
    3337, 3338, 3339, 3340, 3341, 3342, 
    3343, 3344, 3345, 3346, 3347, 3318, 
    3319, 3320, 3322, 3321, 3328, 3324, 
    3323, 3329, 3354, 3378, 3379, 3355, 
    3369, 3371, 3356, 3357, 3358, 3359, 
    3360, 3361, 3362, 3363, 3364, 3365, 
    3366, 3367, 3373, 3375
  ) 
  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 0.00442

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost": 0.263454463,
    "nested_loop": [
      {
        "table": {
          "table_name": "cscart_product_prices",
          "access_type": "range",
          "possible_keys": [
            "usergroup",
            "product_id",
            "lower_limit",
            "usergroup_id",
            "wdbi_product_id_lower_limit_usergroup_id_price_eff1727beeef",
            "wdbi_usergroup_id_lower_limit_product_id_92b7e8f6a250",
            "wdbi_product_id_lower_limit_usergroup_id_price_perc_3b2301d551d0",
            "wdbi_lower_limit_usergroup_id_product_id_b93629431718"
          ],
          "key": "usergroup",
          "key_length": "9",
          "used_key_parts": ["product_id", "usergroup_id", "lower_limit"],
          "loops": 1,
          "rows": 128,
          "cost": 0.22335624,
          "filtered": 20,
          "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.product_id in (3351,78822,3316,3317,2512,3326,3327,3374,3331,3335,3377,3376,3313,3368,3311,3315,3314,3310,3312,3330,3332,3333,3334,3336,3337,3338,3339,3340,3341,3342,3343,3344,3345,3346,3347,3318,3319,3320,3322,3321,3328,3324,3323,3329,3354,3378,3379,3355,3369,3371,3356,3357,3358,3359,3360,3361,3362,3363,3364,3365,3366,3367,3373,3375) and cscart_product_prices.usergroup_id in (0,1)"
        }
      },
      {
        "table": {
          "table_name": "cscart_master_products_storefront_min_price",
          "access_type": "eq_ref",
          "possible_keys": ["PRIMARY"],
          "key": "PRIMARY",
          "key_length": "8",
          "used_key_parts": ["product_id", "storefront_id"],
          "ref": [
            "u985510652_ecartify_abhi.cscart_product_prices.product_id",
            "const"
          ],
          "loops": 25.6,
          "rows": 1,
          "cost": 0.023716864,
          "filtered": 100,
          "attached_condition": "trigcond(cscart_master_products_storefront_min_price.product_id = cscart_product_prices.product_id)"
        }
      }
    ]
  }
}