I would definitely consider that a serious potential issue, if for no other reason than so many communities will likely find a use for tags based on the nature of the community structure.

For example, I could see a ton of communities having tags for things like modposts, new member intros, meta topics, memes, questions, reviews, how-to's/tutorials, guides, etc. and that's just for broad post types that would apply to thousands of communities.

I think letting users manually make their own multi-lems, perhaps with the ability for communities to sort of team up to make uber-lems of closely related communities to help users discover more of them...but sub, unsub, multi, and un-multi as they see fit...is likely the best approach.

But one thing to consider is how divided it would be. Let's say I wanted to browse martial arts so I go to #martialarts. Now what about people adding stuff like #MMA or #karate. None of these would show up in #martialarts. Seems like hashtags would be even more divided than communities to me