Huh, never thought about that. I know my friend rooted and ROM'd her Note 1 and it does lose quite a bit of the S-pen functionality. Not sure how launchers do.
I love Nova! Only reason I initially installed it was to get rid of the damn persistent search bar!
Since I upgraded to Prime, I love the gesture features (among other things). I just swipe down on the screen and it launches the dialer, single tap with two fingers launches the camera etc. I'm able to run with 3 super minimalist homescreens this way.