Re: What are these tables?
I’ve had this concern as well. I hope to one day get to the point where this becomes an issue 
For those that are concerned about the database structure but still want wpmu, there is an effort called lyceum at http://lyceum.ibiblio.org/ that modifies the wpmu codebase to use single tables instead of creating new tables for blogs.
One of the main drawbacks is that plugins that create their own tables need to be modified a bit to support this structure. This would include BP, for sure.
I still don’t have a good sense of how many people are actually using it as it doesn’t seem to have a very active community.
I’d be interested to see if bp could run on top of it and which is more scalable.
