TO sum up.
games that exist as carts are type 1 games. these update fine. the update is a separate free download that installs as a different title. They have to be because the game exists as a cart and that's the only way for an update to install.
type2 games (the update is just the new version of the game, and replaces the old title) cannot update anymore. you have to have a legit ticket. An example type 2 game is VVVVVV. When you buy it from eshop you get latest version automatically. For these you need a new CIA file.