I've read a few books on building WP themes and I certainly understand the basics. I would like to know read up on advanced topics like hooks, wp_rewrite and how functions.php should be structured. Can anyone recommend any good resources?
The best resources available are:
Beyond those three references, I would also recommend that you take a very close look at the structure and composition of the TwentyTen theme that ships with WordPress. It's written by the same team who writes core, so it's your best bet for a "definitive" example of most things WordPress.
I'd also suggest you invest in one of the nicer theme frameworks available - my personal recommendation would be Genesis. If you're using a framework for building your theme, most of the work is done for you. You'll also have more tools at your disposal, and some of the frameworks are incredibly advanced in their design. Looking at how someone has already done something and deciding how you'd improve on it can be one of the easiest ways to learn.