Casual references to Hitler and Naziism are pretty strange and definitely never a sign of anything good. You're either understating the threat by colloquialising it, or outright signaling that it's not a big deal to you (and I say this as someone who has been guilty of this in the past). Casually invoking it for fun and jokes was way, waaaay too normalized even as recently as the 2010s.

This makes it pretty unsurprising from Hussie. An edgy white dude forumite in the early 2000s? Slur it ain't so! Of all the things I blame them for, I do believe they're sincere in their apology when they mention that they wrote the Skaianet lore years and years before they actually posted it and didn't do a good job reviewing.

That being said, I will defend the references in the comic, and the invocation by the readerbase, because the parallels being drawn are deliberate. Homestuck is telling you things about fascism, genocide and eugenics. It'd be like saying it's wrong to call the stormtroopers in Star Wars "stormtroopers". Where my problem with that series lies is that it's watered down the fascism into generic bad-guys that the series still wants you to think are at least a little bit cool. It's a good thing Darth Vader doesn't really dress like a nazi like some of his officers do, otherwise a lot of children's halloween costumes would have faced some serious controversy.