A few hours on the Interweb and suddenly their are plenty of potential ideas and ships crews that have simply disappeared... or dragged below the surface?
1794 HMS Ardent lost with all hands 500 crew – It is presumed that she caught fire and blew up. A part of Ardent's quarter deck with some gunlocks deeply embedded in it was found floating in the area as was splinter netting driven into planking. No trace was ever found of her 500 crew.
1799 HMS Lutine – Sank off Vlieland in heavy weather. She was carrying a large cargo of gold, most which remains unsalvaged. 269 people were lost.
1800 USS Insurgent departed Baltimore 22 July and after a brief stop at Hampton Roads sailed for her station 8 August 1800. Never heard from again, the frigate and her crew were presumed lost as a result of the severe storm.
The possibilities are endless.
I just now need to resist the draw to paint pirates rather than those half finished Frenchmen.