just make sure you set your security on the public access to not access.
when gating off your boat you should hit land and gate from land/pier.
when gating to your boat you should gate from a secure location like your house.
(actually if you gated off your boat i am not sure what would happen if someone entered your gate from the other end)
I have yet to be attacked at sea or had someone blast my boat up but I dont leave anything on my boat either.
when you buy a boat then put the rune into your rune book. it will still work even if you dry dock and drop your boat again into water.
since the key is a rune in your runebook it is much more secure in getting on and off.
I have had the orc boats fire at me as I passed them by a few times hehe