SELECT 
  rate_id, 
  rate_value, 
  destination_id, 
  IF(rate_value = '', 0, 1) as rates_defined, 
  base_rate 
FROM 
  cscart_shipping_rates 
WHERE 
  shipping_id = 3 
  AND destination_id = 9

Query time 0.00392

JSON explain

{
  "query_block": {
    "select_id": 1,
    "nested_loop": [
      {
        "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
        }
      }
    ]
  }
}