No, the "deep web" is real in the sense that there are billions of network addresses that contain content or services which are not accessible through the 'standard' discovery services (Google). In many ways things like Usenet are still part of it as there are netnews groups, and they get used, but there isn't a lot of indexing going on. Further there are at least two 'separated' NNTP type networks that are invitation only.

So it is a "collection" of secret societies, each with their own quirks. As a collection is constitutes a 'web' and perhaps the only commonality is the desire to not be part of the "public" web.

[1] http://begthequestion.info/