fire, bomb and other commands use sectdamage() to damage sectors and their contents. sectdamage() damages land units and planes there, but not ships. This is documented in info version:
Damage to Spills to
Sector People Mater. Ships Planes LandU.
Sector -- 100% 100% 0% 4% 30%
I think a reasonable amount of sector damage should spill to ships.
This feature request is split off [bugs:#53].