Using 100's of schemas in a database SQL2008R2?
One problem you'll have is with SSMS. I have a client with a lot of objects in a single database, and if we expand the Tables node in Object Explorer, SSMS dies. 

As well as this, I suspect your code might need to be changed. Either you need to rely on the default schema for every connection, or else you need to change every query. Hopefully you've been using two-part naming so far, so every dbo.reference will need to change. Far from ideal.

You still have a lot of flexibility over filegroups, which is good, and having a single database might even help avoid disk head movement on the transaction log.

I doubt performance will be affected much either way. But the code changes required could be a huge frustration. And if you need to rely on the default schema, there are extra locks (LCK_M_X) that need to be taken out to work out which objects you're referring to.

I'd be really hesitant to redesign that much, but it really depends on your priorities.