Usually when Nintendo shuts down a fan project, it looks as if it's to stop it from competing with one of their upcoming products.
When the original SMBX site got struck down, Mario Maker appeared a few years later so I think it's safe to say it was in development at the time. Same happened with AM2R as well.
I think they are confident in Mario Maker 2's ability to gather an audience so I don't think they will find it necessary to strike SMBX down a second time...
You found my hidden signature... OH NO!