I've been using Apex for some 3 months and my S pen apps all seem to be working. Apex and Nova are just an overlay of home screen icons. These launchers do not affect the apps as such nor the pen detection. To be noted: this is on a Note 1. I wouldn't see any problem w/ Note 2.
If the info is good, hit the "thanks" - raises my standing in the community!
Honestly, I got nova launcher a couple weeks ago when it was on sale, just so I could use it on my new note2. After installing it, I realized I like the touchwiz better....but I AM using beautiful widget cuz their clocks and weather graphics are awesome.