IMHO hotkeys is something basic. I understand Wayland is being designed with security in mind, but Wayland developers must understand that what they're trying to do is to, ultimately, create an X replacement. And X is, mainly, user-oriented.
You can't have a graphical, user-oriented, server and tell the user to "hey, just use a shell script and a control binary, and then hook a hotkey into your window manager and make it run that script". That's just not how user friendliness works.
Try to find a common ground between Wayland being secure and Wayland being practical.