I have fished in this game a ton and I've seen a lot of boat exploits. I'm going to go ahead and let the cat outta the bag.
"Zaphod brought his boat in front of my boat, and somehow hopped onto my boat."
This exploit is probably how a large majority of all boats are broken into. Basically the exploit works by bringing a boats plank (usually a small boat) directevtly to the front(hull) or (back)tillerman. Once in position all the pirate has to do is open their plank and walk on. It basically creates a bridge to your boat. The best way I have ever combated this is by parking your boat in a manner where no boat can position their plank this way.
If you park in a cove that has equally level land as your boat, and blocks the front and back, There should be no way to access it.
For the record, there is very little secure storage in this era, boat exploits were common. While the above mentioned feature is not intended and will be looked into, there were many other unintended ways to board back on OSI. The only thing that is really secure is your bank. House Secures come a close second as long as you trust your friends list. Houses can be made very secure, but there are still a few legitimate ways that people do find to enter, often to the great surprise and disappointment of the owner.