Bots will be unaffected. In fact, hack client users will not be affected by the unity client, either. It is very likely that old Flash clients will continue to work with the game. Any protocol changes and new features can be reimplemented in the Flash hacked client, rendering all code protection/obfuscation on the Unity client moot.
Edit: Changing the protocol daily would involve having all players redownload the Unity client daily. An alternative to this would be having the protocol change and the server send the clients info on how to communicate with the server… which could also be used by the Flash client.