" But it doesn't take that long to get a weapon up from the magazine to the flight deck."
Then why didn't we cover/protect him?
Politics. As a research vessel the Pueblo should not have had a 50 caliber on it. If the conditions warranted such then the mission had done been compromised. North Korea was likely tracking the ship and Washington knew it thus the order for the 50 caliber I think was done in Toyko before they left out headed toward NK.
I have no idea why Pueblo wasn't covered. One possibility was not having any combat ships close by so as to not draw attention. Technically PUEBLO was a non combat research ship in the eyes of the world. LBJ did a stupid act by placing the 50 caliber onboard to start with. A capable E.D. system would have been a much wiser investment.
If it was that much danger the mission should have been aborted or at least the Captain alerted. The Pentagon knew NK was on the war path though but PUEBLO wasn't privy to some of the later developments and deteriorating conditions as I understand it.