Ah, I see.
In my app messages are sent to the app Nxt ID. But if messages are sent between user Nxt IDs then, yes, we have a problem.
Well, in the spirit of simplicity we could agree that the first 4 bytes is a unique tag for each protocol/application.
Not sure how well such gentlemen agreement would be honored, though.
Another option would be to use kind of "client-server" architecture instead of "peer-to-peer".
I.e. users of an app send AMs (containing destination ID) to the app Nxt ID instead of sending AMs directly to destination ID.