And given to how The Dominion dealt with The Maquis, it's probable that Thomas Riker, along with any other Maquis prisoners, were simply taken out and shot when The Founders started "advising" Cardassia.
Not necessarily, Cardassians do love slave labor. And there's a host of reasons the Founders might not bother to kill them. Leave them as a living example of what happens if you oppose them, make the Cardassians feel they still have power by leaving them prisoners to play with.