I run several sites without sidebars and a few with. In my experience, a simple site doesn't need one, and it can get in the way of showing a user around the page. I do often have horizontal "section" navigation, though. With a Wiki especially, it is often the point that the site is unstructured, with plenty of cross-linking between pages providing the navigation.
To take your question about dw.org, I think it's possible some sort of persistent navigation breaking the Wiki into sections would be useful, but not necessarily as a sidebar. I guess Andreas is happy with the existing index pages like
http://www.dokuwiki.org/dokuwiki and
http://www.dokuwiki.org/manual.
- Iain.