How do you know it doesn't work in Book mode? Has anyone bothered to ask a Nintendo official? have they shown a game in book mode?
If it's using the Sharp Screen like we assume it is, then it is stil;l very possible that it works in bookmode and Nintendo just didn't want to show it off yet (like the port in the back, the OS or UI, the Stylus, the internal storage, Virtual Console, Movie Service[Netflix3D!!!] or the Wifi).