Having addressed the empty forums issue so I can see everything from the front page (I was using containers to segregate the categories with sub-forums) I've encountered another problem.
I don't want anyone to be able to post anything in the top-level category — all posts need to go in the appropriate sub-category. But when I restrict creating/replying permissions for the top-level category (which is no longer a container and has a single post so it shows up on the forum menu page), it prevents users from posting in sub-categories as well.
I suspect I have to re-submit this as a feature request? Because I'm guessing you can only take away permissions in the hierarchy of sub-categories; you can't grant additional permissions that aren't available to the parent category?