Unless it's Sony the one who buys Atlus, I can't see any other buyer against the idea of supporting Nintendo platform(s), especially since Atlus titles sell well on Nintendo hardware (3DS, at least).
The only way I'd see it ending that way is if someone buys them to have them make all phone games.
They're a bit expensive for that, but let's hope Japan Card or whatever that buyer who seemed interested in such a thing doesn't get them.