It probably is out of habit, but technically (very technically) even suspended, Gibbs is still an NCIS employee, at whatever his position is (Team Leader?) They never said if the suspension is with or without pay, but he is still in his position, not sure how benefits would work. And an indefinite suspension can be lifted at any time, whereupon, Gibbs continues as leader of the team.
I suspect McGee is now a Senior Agent (like Tony was). Probably a bump in grade and pay over the other agents, I don't know if he does anything supervisory, like conduct performance reviews, etc.