If we assume (always a mistake) that the person in control of all this is from the future, and they've tagged these guys, it doesn't matter where "the government" has hidden them... But if like in 12 Monkeys, that tagging isn't good enough and they do need an accurate historical fix to "find" their agents... A secret prison that "doesn't exist" is about the only way to go to make sure that these guys ain't going to be recycled and used to wreck chaos here or elsewhen again. Or... Maybe it was Lucy's idea? Is she on a mission from the future or is she bastard enough to have gone rogue after being sent on mission, but then this is like the Dirty Dozen right? Using convicts for Suicide Missions. Stick and the carrot. Have you ever seen someone try to make House do shit? You know, unless Lucy is one of the bastards form the future running the missions. Then her setting up the prison is just making it easier for the future to get bizzy.