I think it will run Android apps but through their own custom OS. Nintendo has been humbled and realizes they can't make people choose against apps.
Plus Nikkei is almost always correct in the end (even when Nintendo denies it). I trust their track record. Beyond that, there's good money for Nintendo to make off Android apps. They will simply just offer them through their eShop where they can control how many apps and which apps are available, and they can take home a 30% cut of those apps.
It will also save Nintendo on functionality cost. For example, why waste developer resources making a video or MP3 player when there are dozens that are available on Android. It would also give the system all the popular social media apps like Facebook/Twitter/Instagram overnight.
