Yes the application handles it correctly (when the mouse event is fired it checks that the right mouse button is clicked and all three modifier keys). It works on windows and linux with gnome(GTK+).
The question was if KDE's error message blaming Qt was correct or not. The global keyboard shortcut setup doesn't even allow me to press e.g. ctrl+shift+alt+A, when I hold down the three modifier keys the error message is shown and the assignment of a shortcut is blocked.

I would assume any good toolkit for handling keyboard input supports all three (alt, shift, ctrl) modifiers keys at the same time. Perhaps I should blame Freebsd in some way, perhaps the combination of these keys is propagated up to Qt as some other strange key combination, not what Qt would expect from ctrl+shift+alt being pressed.