If we are assuming a full kernel level hack on your system then the following is true:
A GUI isn't needed to do anything at all on your computer, everything can be done with pure code.
BUT THEN
If the hacker was also some kind of playful artist, he could create an invisible shell which would mirror your GUI without actually touching it. He would have access to everything, all your windows, their locations, icons, your status bars, desktop, your tabs, everything. And he could manipulate all of it, essentially using your whole computer as if it was his own through his special "GUI copy app" that would take care to never interfere with your GUI.
Window movement, memory reading and writing can all be accomplished through his invisible GUI shell which isn't really your GUI, but is a clone of it with all functions duplicated and mirrored. Probably based on explorer.exe.
Of course he would have to decide whether or not to propagate YOUR GUI manipulations over to his version. He could choose to do so, just to see what you are doing, then override it and go about his business as if he were sitting on the computer in front of you.
Such tool would only be made by somebody who was more interested in making a fun art project rather than getting stuff done.
But is it possible? Absolutely? Has it ever been seen in the wild? I don't think so, only because the hacker priorities don't mix.