I have a Note 2 and Note 10.1. I use Nova Prime on both devices. I can honestly say that the S Pen still works as well as all the other Samsung stuff that goes with it (cascade/split window view, pop up S Note, S Pen launch menu, etc). The only thing you might have issues with would be Samsung dedicated TW widgets. Samsung made sure their widgets don't work well in other launchers other than TW.
So Samsung removed another feature in 4.3? My Note 2 running 4.1.2 can have both swipe and PIN enabled for lock screen. I, too, use shortcuts on the lock screen. Though there is the extra PIN entry step needed to launch the app from lock screen.
You may need to look at a third party lock screen app like WidgetLocker. Might be something you are looking for. I never used it so not sure.