>Still not sure why for a Web Directory the conception of "deep link" is important.
The most critical part of a web directory design is the treatment of deeplinks. Taxonomy, site descriptions, etc., can all be developed with help from analogies in other fields. But how deep links are handled determines whether a directory is useful or feasible. Too many deeplinks, not practical to build. Too few, pointless to use.
That "happy medium" doesn't fall in exactly the same place in every category, and it usually takes quite a bit of experience to know where to draw the line. I personally built up a lot of Arts categories from scratch, and have a good feel for the line there. But although I'm a programmer I don't edit much in Computers (partly because I never had a small category to build up while learning the ropes, and when I was starting out I really disagreed with the approach taken as I understood it. FTR, either my understanding has grown or the approach has been somewhat modifed, perhaps both.)
This is not an issue you can resolve based on one site, especially not if you have a strong emotional or financial interest in it. You need to have tried to sort out thousands of sites, side by side, trying to make access to each of them appropriate to their content. It's hard, even for humans.