People are not using them because the implementation sucks, their really only being used as gold banks atm for corps to store all their gold, look around a freeport away from the dock and youll find little groups of them full of gold, little 100% safe banks.
To be fair im not against banking gold, players still need to get it too and from the free port so its still at risk while in transit.
In terms of the shops there are a few issues, first of all their free form placement, I think the devs need to build out actual towns on the freeport islands, towns with shops already in place like a little highstreet, and then let players rent the store front and then put their things in for sale, with an existing highstreet/small town everyone will know where the shops are by default and it will encourage players to look around and shop around for things to buy, I think players should be able to fast travel to a tavern in the new free port towns so then can travel over look through the shops when ever they want, we can already do that via death but thats clunky having like a global bed inside a tavern or something would be a much better way of doing it.
Shops could be a huge thing specially with all the blue prints and rare items, we could use an auction house as well.
This game is far from being finished, I just hope the devs have the time and motivation to actually flesh it out.