I honestly don't know, Ryan-Palmsy. I never even heard of the ship or the supposed conspiracy theory concerning it until I read your hub (which was well written and amusing).
I did a quick search on it and as far as I can tell the story you present is pretty much what it is out there in the area of the more easily accessed information. Perhaps one day I will get around to checking it out and dig for the original resource material in order to formulate an opinion on the matter, if I should find myself interested enough in that particular incident.
All I currently have to go on is a few facts and a few people who believe they have a correct interpretation of those facts, so as you can imagine I am in no position to formulate any sort of meaningful opinion on the matter. I am open to any possibility though, regardless of what I or others may think of the conclusion or the feasibility of it, even after I have formulated an opinion (should I one day do such).
But, if I were asked to take a stab at what happened based upon my extremely limited knowledge of the subject and based upon pretty much one angle of the story (the one you presented), I would have to concur with you that it likely went down due to a major storm system somehow sinking the overloaded vessel, or that perhaps a rogue wave was the culprit.