Is it normal that switching through workspaces with CTRL +alt +left/right/up/down doesn't work when I close the last window on the active desktop?
Is there a way to alter this behavior?
Have you set nautilus to not draw the desktop? To find that out, run this command:
If it returns true, then its a bug. I know you've filed this bug and I'm the guy who commented there.
If it returns false, then its a known issue in Unity, to not un-focus closed windows when Nautilus is not running (currently it depends on Nautilus to take away focus from the closed application).
It is highly likely that something is messing up the focus tracking.