If they had kept the late 90s or early 2000s aesthetic, then most people would've assumed that it was sti one of those hobby projects more focused on a nostalgic (but not necessarily better in any actual way) technological aesthetic that certain tech people get really attached to, and not something that was meant for serious use and to be pleasant to use in the modern decade for people who prefer modern interface paradigms. Having a clean and well-designed website that's nice to look at and doesn't feel horribly outdated is a good move in my opinion — to me, it signaled that the project really has shifted its mentality and goals in a substantial way and is now looking towards the future instead of the past. As soon as I saw the new website design, I got excited because it confirmed for me that their mentality has changed and that this could be something that could really go somewhere.

Maybe you've learned to associate a nicely designed website that's pleasant to look at with short lived projects that are worth avoiding, but I think that's more your problem:

Maybe you should realize that most new things don't last very long and so of course websites that are designed in a new and modern way will often be for projects that don't live very long simply because new projects are more likely to use a modern website design, and they are also likely for unrelated reasons to only live a short time.

And that these exact same pressures and considerations would have applied back in the 2000s or 1990s, such that back in those days oldheads might have looked at something with a 2000s or 1990s design and thought that was clear evidence that it wouldn't last very long, because most new projects made back then would have been made with contemporary design styles, and would have also not lasted very long simply because they were new, same as in the modern day.

And that your association of long-lived products with 1990s and 2000s design aesthetics might simply be survivor bias: most long-lived software projects today 1st started in the 90s or early 2000s, at the very least, because that's just the first set of decades that are long enough ago for projects that were started then and still survived today to be considered long-lived. And so, of course, most long-lived projects you are familiar with in the current decade will have aesthetics from decades ago, because that's simply how longevity works. And so you've learned to associate longevity with an old aesthetic, but there's nothing really about the aesthetic that talks about or portrays a mentality that makes projects live longer. It's simply that longer-lived projects will be from an older era of aesthetics. But there were plenty of projects that were designed with 1990s and 2000s aesthetic sensibilities (and whatever magical philosophy you attribute underneath those) that didn't survive long at all, just the same as projects that were designed with modern sensibilities that don't last long, you're just not aware of them because they didn't last and so they didn't show up in your sample.

Edit: It occurs to me that this comment probably comes off as overly hostile and confrontational for no real reason, so I do want to apologize for that. I'm in a very grumpy mood today. I think my reasoning is correct, but I do want to clarify that you're totally allowed to prefer 1990s and 2000s aesthetics. Personally, I like both modern and 1990s aesthetics (in websites specifically) roughly equally and for their own unique reasons. ,the reason I made this comment is just that I find the cargo culting of ancient technical aesthetics[1], as if they are not only indicators of good software in and of themselves, but also of some moral purity and improved moral fibre on the part of those who use them, very tiring. There are many things wrong with our modern technical aesthetics to be sure, but I think there is an almost equal amount wrong with the sort of older technical aesthetics that people tend to worship, like the Unix philosophy and its associated tools and development environment, and things like that. They are just different kinds of wrong.

[1]: https://prog21.dadgum.com/74.html