I haven't been able to find a contributed module that might make this easier, so the only other possibility is code.
What you are basically asking for is the altering of an existing route, that was defined by the User module.
I'm not sure how much experience you have with the new Drupal 8 architecture and APIs, so I'm going to just dump a few links here :p
The first is the documentation of the new routing system that Drupal 8 is using.
The route that you want to change is the one with the path /user/register, so you will have to look for the route's name and alter it.
A good article about how to do that can be found here. Your use-case is very similar to what the example shows with the logout route.
So basically you will have to write a RouteSubscriber that will alter your route, based on the current user's loggedIn status. I'm not at my PC at the moment, so I can't give code example, but if you need, then I can share a solution.
Be advised, that there are lots of new concepts that you will have to understand first, but if you already know Drupal 8, then you will have no problem with the aforementioned solution.
Another possibility would be to hide the link from the theme layer, in a Account Menu's preprocess function.