I personally don't think this is a huge issue, but it is an issue. I usually pick the biggest community on a topic, or if there are multiple that are fairly active, subscribe to both/all. The only real complaint I have about it is that users will often make the same post to both communities, so I see duplicate posts on my timeline and the discussion is split in half.

I do think it would be nice if there was a way for community mods to choose to combine two communities across instances, in a way that they would appear as a single community to users. I don't know how that would be implemented though.