So I just read Theymos' post in the Auction board: https://bitcointalk.org/index.php?topic=5407725.msg60976136#msg60976136 but it's locked so nobody can comment there, and it wouldn't bode well to start a discussion there anyway since you can't delete or edit posts there.

So, ads are not going to be auctioned away anymore. He did mention that you can privately contact him to buy some ad slots from him in the usual manner.

Seeing as this frees up a bunch of ad slots, what does Theymos think of advertising non-profit bitcoin sites?

I was thinking in particular about websites like bitcoin.org and perhaps my own website bitcoincleanup.com. Of course, as a prerequisite you must already have an HTML banner designed.