Nip89 enables organic discovery of apps from within whatever nostr client you are using. You could build an app store type experience with nip89, but I think it would be redundant.

App links are not added to notes, nothing about notes needs to change in order to use nip89.

The key point is that when an event cannot be opened by the client you are using, it will let you open it in a client designed for that specific event kind, and it will get this list of clients from the people you follow.