Of course it could have been Jack during his 2 missing years...As I said in another threar it's doubtful it's Jack.
1. Jack's no longer in the 51st Century, so if it is him then he had his hand cut off before the events of The Empty Child/The Doctor Dances and I think we'd have noticed. People will shout timey wimey here but the big blue guy did say it came off the arm of a Time Agent, again Jack hasn't been a Time Agent since before he met the Doctor.
2. Jack's vortex manipulator was pretty much deactivated by the Doctor at the end of Last of the Timelords.
Much like James Bond isn't the only 00 Agent, JAck Harkness isn't/wasn't the only Time Agent, there were likely quite a few of them.
True, and I guess 51st Century technology could have given him a new hand before we met him, but seriously isn't the simplest explanation that the VM and the arm, belonged to AN Other Time Agent?