Given the bones of the crew were found at their seats and not piled up by the hatch it is speculated the crew asphyxiated. she backed off and, after the explosion, they were to row back but it was against the tide and everyone was tired from rowing out so she drifted and everyone just fell asleep. Housatonic bottomed out with much of the rigging above sea leval and later declared a hazaed to navigation and blown up. I have been to Hunley and the Confederate cemetery where the remains of 3 crews are buried
I had read that they asphyxiated, too. They had to use oil lamps to see what they were doing. That, and no outside air coming in is an easy way to suffocate.