yeah I feel like the only fangames that get taken down by Nintendo are huge ones like Pokemon (Uranium is still available anyway, thanks fandom), although I'm sure that's more-so the Pokemon Company themselves, but the other Mother fangames were never taken down, I feel like the work the Mother 4 team is putting into rebranding and redoing things because of the rebrand may be unnecessary. I wouldn't even be surprised if Nintendo couldn't actually take the game down without Itoi's input, and him allowing the fangame to exist.
That being said I'm sure it'll still be good, but I wish they could've kept some of the original Mother enemies and characters like Starmen and Mr. Saturn. They seem to still be working on it based on the fangame's subreddit, however they don't say anything about internal issues between each other or even act like there are any, so I can't tell what's going on with that. All I know is that apparently some guy they worked with, who left the team, leaked an outdated script or something on 4chan (just based on what I read today).