No, just $3 for the Android purchases. Since it was made on another platform, Apple doesn't get a cut.
I thought the way it worked is: - User buys game on 3DS, links to their Nintendo account, can play on 3DS, iOS, and Android. Nintendo gets $10. - User buys game on iOS, links to their Nintendo account, can play on 3DS, iOS, and Android. Apple gets $3, Nintendo gets $7 - User buys game on Android, links to their Nintendo account, can play on 3DS, iOS, and Android. Google gets $3, Nintendo gets $7