This is a topic that has been bugging me for some time now, and as I have not found a single post out there telling me otherwise I'll just go ahead and rant out aloud!
In WSS you have effectively two ways of storing files. either by uploading the files into a document library which is available via web, webdav and SharePoint Designer or via adding the files to a folder created through either webdav or SharePoint Designer (not via web). Each teamsite comes with such a built in images folder.
I have found that these "hidden" folders do have their use. Namely for images and files that are used for design purposes only. If your WSS site is using several images to make the site look pretty, those folders will keep them away from the main content of your WSS site and keep them nicely separated.
That way you only use document libraries for documents relevant to your enterprise and not for designing the WSs site. The biggest benefit in my eyes is hiding away those files from end users who might accidentally decide to move or delete the files and ruin your site.
The drawback is that you won't have the power of versioning and check in-out as youhave with libraries. But then how much versioning do you need for your gifs and jpgs? the master page is the one you want to worry about!