SELECT 
  rate_id, 
  shipping_id, 
  rate_value, 
  destination_id, 
  base_rate 
FROM 
  cscart_shipping_rates 
WHERE 
  shipping_id = 6 
  AND destination_id = 12 
ORDER BY 
  destination_id desc

Query time 0.00036

JSON explain

{
  "query_block": {
    "select_id": 1,
    "table": {
      "table_name": "cscart_shipping_rates",
      "access_type": "const",
      "possible_keys": ["shipping_rate"],
      "key": "shipping_rate",
      "key_length": "6",
      "used_key_parts": ["shipping_id", "destination_id"],
      "ref": ["const", "const"],
      "rows": 1,
      "filtered": 100
    }
  }
}