It kind of has. URLs have the notion of paths, which are obviously strongly associated with the notion of file system hierarchies. People sometimes (sometimes accidentally) put their file systems directly on the web, see DirectoryIndex in apache for example.
> Why isn't a website just a remote directory on someone's computer that we can explore via a file browser?
Well now we are getting into the meat of it. To be a hypermedia requires the presence of hypermedia controls in a media. Hypermedia controls can be as simple as links, but the web introduced more sophisticated controls such as forms, and allowed HTML authors to specify more significant interactions beyond click-to-link.
IMO the uniform interface is the most interesting aspect of hypermedia, and that really emerged post Web. I like the authors concept of a file explorer enhanced with hypermedia ideas though and would be interested to see more details on it.