This is where speculation begins. I believe that this could be related to the Nintendo Switch App coming to mobile phones. This may allows players to check-in on what games they are playing or planning to play online. This is to notify your friends and/or nearby players if they are looking to play the same. Therefore, they could decide to join you afterwards upon seeing the notification. This also may allow players to invite others to join them. This is thought is derived from what we have seen on the new SplatNet that Nintendo showed in the most recent Nintendo Direct broadcast focused on Splatoon 2.
Of course, this is but an idea as to what Nintendo could be planning to do with this Nintendo Check-In. The Nintendo Switch App will be making its appearance on the mobile app stores soon enough and we should hear more as to what will be possible to do with it. As we already know, the app will have something to do with Splatoon 2 off the bat.
No doubt this app will continue to evolve and grow with upcoming games. For now, the focus is on Splatoon 2 as it is very close to release now. Stay tuned for more info regarding Nintendo Check-In. In the meantime, let us know what you think this service will be about in the comments below.