hmm well an idea of mine was to have the captain of my vessel from a family heavily rooted and supportive of a particular religion/cult and that would influence how his ship runs, mandatory sermons, screening new crew to ensure only faithful are permitted to serve aboard. And as the ship underwent it's numerous re-fittings and repairs over the last thousand years it influenced how the ship looks. Gothic angels/ gargoyles or whatever as figureheads and even gun ports. Added probably on the dime of the my characters family.  

I don't know. it's either that or something else.