it sure seemed like some of the shit on Freenet was as dark (both in content as well as buried deep) as anything on Tor
Of course. Everything new was old already.
Before the TCP/IP Internet even existed there were distinct categories of content on BBSes and other online repositories, with a range of "locatability", from well-indexed items that were easy to find and mostly relatively uncontroversial, to illegal or offensive material that generally was found only by word of mouth. Many BBS subcultures had materials in various categories - the "txtfile" hack / crack / freak culture is a good example.
The same goes for the pre-web Internet - even more so, because now there were more participants, faster connections, more storage, and a wider variety of indexing systems (Archie, WAIS, Gopher) that could be manipulated in various ways to produce public and secret repositories.
Prior to modern IT, of course, there have been secret presses and bookstores and the like pretty much since written language was invented.
The "dark web" (an obnoxious term, but it's what we're stuck with) is interesting in its particulars, but it's certainly not a new phenomenon in general.