That is a possibility, though most apps don't use Bonjour.
What most apps do is store or copy their data onto an internet server, and the corresponding app fetches it from the server. iStudiez does this. The app then allows users to set up an account on the server the first time the app is run.
Bonjour does not store anything on a sever, it only allows direct communication between two devices. With Bonjour, both Apps have to be connected to the same network, and you have to specifically connect them and then send/receive each time.