For my flat structured site with 1500 purposely empty categories, I have figured out a way to get search engines to index it.
I transclude parts of Special:Allpages to http://radioscanningtw.jidanni.org/index.php?title=%E6%A8%A3%E6%9D%BF%E8%A8%... which I link from my user page which is linked from the main page.