Quoted from VacFink:
That said, if you were a secretive organization like the masons, and needed to get to something hidden in plain sight, this is how you would go about it
Thought crossed my mind as well because:
1) The theory that it was done by pirates is imho just ridiculous, the reason pirates would steal it to begin with it, for survival, money to trade with, living. I just can't fathom they would go to such lengths for something they damn well knew they'd be retrieving in short order. Also do you think trust within all the crew(s) involved would, or could be a viable stance to take given they could come back and get it on their own, or even worse, tell some others about it because of the need for help in retrieval.
2) This feels a little bit better but with all that is known about their activities as a secret organization, coupled with the fact should any of them be captured and tortured they may break and tell where those precious items are. Crazy sounding,hardly, think about all the atrocities the church has committed in the past to gain information; that being said I hardly think this would not be one of the things critical to keeping these sacred objects safe. That leads to me to believe that if it were them, they would remove it and deposit it in other locations to thwart any attempts to gain access and the best way.....keep it in motion. In all these theories I try to keep in mind the number of people this would have required and what do you do with all who have knowledge, well kill all of them, which may very well explain the bones found. I can think of no other sure way they could have kept a secret with so many involved. The Egyptians and their secret tombs come to mind.....they often killed those involved to assure location would remain unknown.
3) Not much to think about here for me as evidence is nonexistent upon the North American continent that any Romans ever sailed this far across the Atlantic or Pacific oceans. The concrete, although a Roman invention would have become wide spread knowledge within a year or two at best after it's initial use. So for the concrete, knowledge of the use of lime etc. is all that's necessary to explain it's being there. Sword was a fake so has no bearing on anything.
I personally still feel the U-shaped structures and all were built in order to either build new ships or simply repair and maintain those present so that are ready to deploy. Makes sense that this applies to any of the theories above as all rely on stealth and possible need to escape should it be necessary.....remember the Templars/Masons specially would have more likely than not have people (church etc) searching for them. A semi-dry dock would have allowed them to somewhat hide partially their ships from prying eyes as reasonably as is possible. Safe no, but better than anchoring off shore like a beacon saying here we are.
Last but not least maybe there was something there temporarily and has been removed and all there is left for us is some very interesting history that to me is treasure in itself.