I get this here as well!
It happens at random, usually when I play around with my MIDI keyboard on an AIR synth, without recording or anything, just playing. After about 15-20 minutes GUI freezes but I can still play notes on my keyboard.
When I try to kill Cubase using the task manager it closes the window but the process keeps on running. I tried to disconnect my audio interface, that didn’t help, but when I powered off my MIDI keyboard the process died. This does not mean necessarily that the freezing is related to my MIDI keyboard. After all, IIRC, it also happened to me while mixing a few months ago. You mentioned it happens when you tweak with plugins, maybe it’s the same with the AIR plugin in my case.
Did anyone encounter it again or solved it somehow?
I will try the ASIO guard tip.