I have a 3DS, I have a WiiU, and I still wouldn't want Nintendo to own Atlus.
I would hope that Atlus can keep publishing games on whatever platform makes sense for each game.
Unfortunately I don't have numbers on hand, but I do remember seeing them in another thread and the gaming side was making more or similar (can't quite remember which) profit in recent years. I'm willing to eat crow if I see numbers, but I'm pretty sure Sega are doing pretty damn well for themselves.