Ooops, I just realised that I've never read the manual past the key bindings section. The rest of the manual does indeed answer many of my questions.
Whilst I'm playing this, my mind is whirling with things that could improve it; I've already posted a couple here so far. Others include hostile aircraft that are armed and can cause you damage (you've already said armed warships are a possibility, the aircraft would just be faster moving sprites that are not torpedo-targetabble.) Also, sound effects would boost the atmosphere. Some general submarine-like hubbub would be good, along with clankings when repairs are being carried out, and alarms to signify emergency situations. A good list of appropriate alarms can be found here:
http://en.wikipedia.org/wiki/Alarms_...ed_States_Navy
with downloadable sound effect files for you to listen to (in .ogx format).
Personally I would have the Diving alarm/Cow Fart for diving, Collision alarm for collision/flooding, Missile Jettison for fire/radiation, Missile Emergency for inbound aircraft (if you are on or near the surface with radar on) and Power Plant Casualty for mechanical failures.
Hopefully my ideas are of some use, otherwise feel free to ignore them and write them off as the product of a fevered imagination.
