That's just the way things work when humans self-organize. There is the appearance of structure at the beginning, because there just aren't that many people with shared interests. Then as people are unsuccessful in finding the community they'd like (assuming they even looked!) more are created. Then more people come in and mill about and browse and get overwhelmed by the search for a needle in a haystack, so they create more.

Eventually, some communities reach a critical mass and a bunch of small ones fade away into near irrelevance or disappear completely.

As far as I know, the only way to put the brakes on community over-proliferation (if that's even a real thing!) is to add a bit of friction to the creation process. Many kinds of friction devolve into centralization and gatekeeping, so they tend to be avoided in projects like this.

The only kind of friction that I can see working and gaining acceptance would be some kind of "have you tried these communities?" auto-search during the creation process. Simply asking people to search first is unproductive for two reasons. First, people are notoriously bad at imagining that someone else might have thought of something first, especially when they are only person they know with that particular interest. (I've only met a dozen other programmers in 43 years. In my entire life (66) I've not met a single person with even a passing interest in boatbuilding, let alone an actual boatbuilder, etc). Second, even if they consider that someone else thought of it first, people are notoriously bad at searching.