The no deck gun slots appears to be a problem only certain people have and other people NEVER have. The typical questions to ask: Are you playing the latest patch playing from an autosave in port after applying the latest patch, and are you using any mods? Try reverting back to your last port autosave and see if you have gun slots.
Last, when all else fails, start a new career from a clean-no-mod-latest-patch version of the game.
As far as patrol requirements, see if the thread "
how do u patrol off the marshall islands mission?" answers the question.
http://www.subsim.com/radioroom/showthread.php?t=121480
-Pv-