In order to get people to make shops in the black market, there would have to be some incentive for shoppers to buy from stores (though I haven't come up with any ideas that aren't easily abusable, e.g. discount, exp are all abusable). As a separate idea, is it possible to add super strong guard NPCs - that attack anyone who attacks another player first?
Also you'd have to eliminate the shops around spawn (which would make a lot of people upset) but it's what needs to be done if you want the black market to be viable. Give people some time to move their stuff, then wipe the area and make it a ring of no-build with pvp-on. Even then people will trade in spawn even more then, rather than risk pvp.
Overall though, I think the black market is an interesting idea that was doomed to fail.