I emailed Matt Mullenweg, and he explained that the reason for the massive theme purge was that there was a lot of spammy SEO links as well as various violations of the GPL that is required to be hosted in the directory. He also said this, to address the people who are worried about what is really going on with the theme directory:
There were also a few that violated WP community guidelines, like the domain policy. So since Monday we’ve been clearing stuff out en mass. If you’re kosher with the GPL and don’t claim or promote otherwise on your site and your theme was removed, it was probably a mistake. Give us a week to catch up with the bad stuff and then drop a note.
So there you have it. Mystery solved, hopefully. The whole thing is, however, a reminder that a theme marketplace is needed, although I would say that it might be a better idea to offer links to the ones that have already established themselves, given how late to the game a WordPress hosted one would be.