I don't think all android apps work, but tons do (others will be able to answer this better as I never used many apps).
I bought a warranty from Square Trade and they do not care if your NC is rooted or not, they will honour the warranty regardless. And honestly,
most of the B&N staff and/or customer service reps don't know much more than the basic stuff. any problems I had neither the staff or CS reps could help with. It was here at MR that I found my help.