I could possibly see the argument for locking them up as an iOS exclusive -- but Apple doesn't need to buy the cow, so to speak, to get that milk.
That seems exceedingly unlikely without Apple doing something equivalent to a takeover. Nintendo does not release its games outside of its platforms. Nintendo wants the 3DS to be your mobile gaming platform, not iOS.
Nintendo, being a hardware company like Apple, would much rather you buy its games on 3DS (or whatever future system) than on iOS devices. But it may not have that choice indefinitely. Its hardware sales (Wii U and 3DS) have been in freefall. Its software is the one bright spot in its portfolio right now. Its overall financial health is tenuous.
Regardless, I don't really have a position on whether or not Nintendo should make iOS games. I'm addressing the "Should Apple buy Nintendo?" argument, to which my position is "Why?" Absent some sort of fire-sale opportunity to scoop up Nintendo if/when it approaches collapse, or to buy it on the cheap in a defensive move against Android, I don't see the pressing need.
Killer argument. Apple doesn't need to buy Nintendo. Nintendo needs to choose to do just what Apple would make 'em do anyway: create/port games for iOS. If Nintendo goes there either way, they win ... and Apple gets 30% with zero effort.
It would be interesting, thats for sure.