Because although the nanites repair damage, they cannot prevent aging. He had been on that ship a horrifyingly long time. (That's not hyperbole. Stay with me and you'll see why I chose the adverb.)
One of the things I enjoy about this show is how much credit it gives the viewers. Not everything is spelled out.
When we saw the video of the doctor before she committed suicide, she was referred to as Prisoner 23B. D'avin was identified as prisoner 248A. Dutch was identified as prisoner 248B. So we know the count was #A through #B, sequentially. Math is not my strong suit but that means around 5,800 people had boarded the ship and been killed by the interrogation system! Horrifying.
