You used to have to worry about having query strings in your public urls, because search engines would not index them, for fear of falling into an infinitly deep sub-web.
Google now indexes any link on your page, even javascript links. However, they only go to a certain depth on any site now. They believe that any content of importance is within a few levels of an index page.
I haven't figured out how they know what an index page is, but it is interesting to listen to them pontificate on their bot technology. Put up a large site and eventually googlebot will visit like _Attack of the Clones_.
This might have implications for using pages like index.vuh, where the same page will occur at different depths, or under many subdirectories in a package. I don't think robots.txt allows wildcards in the path portion of a url.