That's true, no reason for C'Boath to have been public knowledge. Vader probably didn't even know about him, it's not like Sith are open and honest with each other. Also, it should be noted that palpatine got (or at least tried to get) DNA samples from all the Jedi on outbound flight.
But, there were clones in another book, and while I don't remember the time period, they were definitely in a long abandoned Imperial research lab, so I assume they were from before the Emp died. Can't remember which book it was, so for all I know it was another force unleashed book and these are the same ones you're talking about. I recall these clones being sorta cray cray and possibly deformed. They had lightsabers, but the crystals were bad, so the blade was more like a flame. They needed some kind of medicine to stay alive, so when they managed to steal a ship, they headed to someplace they thought they could find medicine. Does any of that sound like the Force Unleashed stuff?