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.
There's also the small matter of all the signs that tell you what lane you want being jammed up in the girders, so you can't even see them except for 0.5 seconds when you're almost directly under them.
...of course there's not enough room in the picture to add that bit, which seems like a bit of a metaphor.