Why not use a coalesce
SELECT r.ID AS ShippingRateID, r.Name, coalesce(e.cost, r.defaultprice)
FROM shipping r LEFT JOIN shippingexceptions e ON r.ID = e.ShippingRateID
WHERE e.ProductID = 48
This way, if e.rate is null, r.rate is used.
You also should put your e.ProductId on the join so it doesn't force you to select only products with exceptions
SELECT r.ID AS ShippingRateID, r.Name, coalesce(e.cost, r.defaultprice)
FROM shipping r LEFT JOIN shippingexceptions e ON r.ID = e.ShippingRateID and e.ProductID = 48