I think he's hot. (Perhaps it's the hooves? #yestallmen)
In theory, the guy with the three pips in "Magic to Make" whom Mudd guns down at the shuttlebay could be our elusive Chief Medical Officer, alive and active (even if unseen) through at least the entire S1 and perhaps parts of S2.
In theory, Nhan could be our Chief Security Officer for all of S2, never having been an engineer at all (the transporter operator would just be mistaken in "Brother", what with garbled comms and all); we still wouldn't know who initially succeeded Tyler for the first half of "Brother", but at least we're not having much of a gap anywhere else. In practice, Nhan is absent till the start of "An Obol for Charon", being rather explicitly introduced back to the circle of top officers, so we do have a gap.
It's just that we don't have any sort of a theory for the Chief Engineering Officer. He or she can't be any of the characters seen, because all of those are always accounted for and otherwise engaged when a reference to the mystery CEO is made. No high-ranking extras are ever spotted in bronze, either.
Then again, we now have plenty of reason to believe the ship has at least two major engine rooms, one refitted for spore stuff but the other probably still powering the ship for warp and impulse flight. Perhaps the haphazardly cobbled-together flying lab is in need of constant engineering attention and the CEO hasn't left Starboard Engineering since the ship first sailed? (Probably it was him or her who raised the shields in "Such Sweet Sorrow I", having been left behind!)
We did return to the Ba'ul in the finale: the Kelpien have now stolen their fightercraft, so it's pretty clear there have been changes. The planet already has a history of such things, so we can probably predict neat and tidy genocide again, with the Kelpien eating all the Ba'ul just as originally. That is, unless an alien again intervenes on behalf of the underdogs.
Timo Saloniemi