I think it will for the most part sort itself out. I do see this issue has been brought up before but didn't get much traction.
https://github.com/LemmyNet/lemmy/issues/818
I think that something like being able to group communities by topics would help a lot. You could then just sub to all communities that are tagged with the topic, then the fragmentation really doesn't matter nearly as much. Posts would get spread out across communities and instances (which I think is a good thing) but would still have a decent amount of visibility.