The episode worded things a bit sloppily. Knowledge of the Omega molecule wouldn't just be limited to captains and flag officers, Janeway says that when Omega is discovered in the Alpha Quadrant a specialized team is sent in to deal with it. It's doubtful this team consists only of Captains and Admirals. Also, we need to consider starship captains who might hold a rank lower than Captain. More likely everyone Captain and above is briefed about Omega, as are officers of lower ranks who become starship captains. Although, anyone with a lower rank is doubtless informed if they are deemed need to know.
Although, to answer your specific point, I guess had Janeway been lost and Chakotay assumed command of the ship, he likely wouldn't know anything about Omega, unless Janeway had an emergency packet prepared with info on Omega included within. Doubtful Cavit knew about it, unless he had history with these specialized teams that deal with Omega.