If I'm captain of Bluebird, these 16-odd souls are all I have; the only body I can spare is the mascot, and he's a cat - and then I'd have to deal with mice. I'm not going to want to use them for anything short of a Class-A+ "all-that-stands-between-you-and-utter-disaster" emergency. However, I'm going to make very sure that my crew knows the basics of loading and firing a gun, against the remote possibility that that may be all that stands between my ship and utter disaster.
And so would I. But not all captains are as smart as you and I.
Both Book-2 and High Guard list gun combat as a skill that can be acquired by certain navy personnel. I'd warrant that a lot of those folk got that training - and likely never had to use it - while on some little destroyer or escort under a commander who believed in being prepared.
Gun Combat is also a skill that not all navy personnel acquire. It's a branch skill for Line/Crew, Flight, and Gunnery, but it's not something you can get on Navy Life, Shore Duty Life, or (significantly) Shipboard Life. So apparently noone in Engineering, Medical, and Technical gets that sort of training -- which implies that nobody trains his entire crew in gun handling.
(Note: I'd totally accept a ship captain who exercised his entire crew in gun combat as an element in an adventure, but apparently such cases are rare enough to fall below the resolution of the advanced character generation system.)
Hans