Just uneducated speculation on my side here but face tracking is kinda cpu intensive isn't it? So it would make sense that Nintendo would use the new second cpu core for that task to not slow down games. Maybe after the softreboot the second core didn't wake up or something like that?
Face tracking is handled by a separate module completely and not very 'cpu intensive'.
I don't think there's likely any slowdown, I'm pretty excited for some nice n3ds 'exclusive' homebrew though










