The idea that a navy vessel wouldn't be equipped to provide its own security in port or dispatch an armed team on a launch is a non-starter.

Because submarines are still ships that can be boarded. This is more for defense of the crew vs offense.

Primarily in case a KGB agent (incognito as a cook's mate) wants to stop a mutiny lead by a group of officers and aided by the CIA.

Possibility of mutiny, sabotage or just someone becoming dangerous because of personal conflicts or mental illness.

If that's what the mission requires, yes of course.

Of course, other aspects of other missions might also require firearms.

And since they have fucking nukes, all possible scales of violence are literally on the table.

I grew up watching Voyage to the Bottom of the Sea... those guys were always needing to break out the small arms. Apparently lots of rowdy sea critters looking to get in the boat.

Defense while docked at port.