"includes every description of watercraft or other artificial contrivance used, or capable of being used, as a means of transportation on the waters of the United States." (I copied it from 33 CFR 159.3, but it's the same wording throughout all the parts of the CFR pertaining to boats).
That would mean that his "floating box" with no engine or other means of propulsion, never had any, not was even designed to have any means of propulsion, is not a vessel....and I dunno know how any court could have found that it was 'cuz the CFR makes it pretty clear what is...and federal law trumps state law.
However, had it been designed to be one, but only had its engines, masts or other means of propulsion removed, it WOULD still be a boat because it's capable of being used as transportation.
So IMO (whatever THAT'S worth), his floating home wasn't subject to any laws pertaining to vessels, but that doesn't mean that it wasn't subject to marina rules requiring that any floating structure moored on its property be capable of moving out under its own power, insured, etc. So the marina did have the right to evict him. As to why the structure was destroyed after it was moved...I suspect there's a part of this story we haven't heard yet. And I'll bet he'd removed all his possessions and abandoned it before it was destroyed.