Lets face it, defending your ships while offline or online is a major deal. Especially once you've made your self some good ole enemies. Now as it stands, the best thing you can use to do this are the large stone gates. These are ugly and also ineffective in the deeper and rocky waters. On top of this, you cannot build ANYTHING on rock underwater. This prevents building in many locations. Myself, along with many many people I have discussed this with, have concluded that two things could fix this. Firstly, the ability to build foundations on underwater rocks. Second, add some more harbor related buildings, like larger walls, better docks for parking, etc.
In all honesty, these gate spams are ugly as all hell, and dont work half the time. Along with this, the underwater rocks stunts any form of creativity in building actual buildings in harbors. Fin.