It's not unusual for sites to still be getting crawled.
Always keep sites clean, I understand a directory index that shows the file structure only is a hole that can be exploited. You can do pages with links to other parts of the site or the index page and use <meta name="robots" content="noindex,nofollow">
The October Everflux thread [webmasterworld.com] already started. Let us know if you see any immediate changes as a result of this, we like to keep track.