I wouldn't be so sure about that. They might be smart and tie smartphone usage to the console similar to Sony remote play and Xbox's smartglass, but with more depth, but I imagine they're able to appreciate the separation of what makes this app popular against what a console needs to succeed. Hopefully, the NX is not heavily dependent on a gimmick which will age.
Also, AR is a long way from being what makes PoGo popular IMO. It's the collectability, real world/outdoors nature and self-generated social aspect. Everyone I know turns AR off most of the time to save battery.