http://wayland.freedesktop.org/architecture.html
The document explains that the Wayland compositor, when receiving an input event coming from the kernel input drivers, decides which window has to receive the event and sends it to the application.
If it really works that way, native Wayland clients could be isolated from other clients and they would not receive input events directed to another client. But, in practice, the Wayland server could have facilities for clients to register and receive all the events, so I'm not sure how all of this would turn out.