That's not entirely true. Nintendo only ever takes down 1% of fangames, typically only ones that are remakes of existing Nintendo games or ones that are monetized (SMBS is neither). I'd recommend checking out this video covering Nintendo's history with fangames and DMCA's if you're interested: https://www.youtube.com/watch?v=OjKWKxYrUWs
If for some reason Nintendo does decide to strike down SMBS, though, I'll likely just reskin it or reuse the base engine for a different game.