Where else would they be?
In the second sinking, when H.L. Hunley, himself stuck the bow of the Hunley down into the mud of Charleston Harbor (and, forgot to close his forward ballast fill valve) the bodies of the panicked crew were found clustered around the (un-openable) aft access hatch.
The point was, the final crew showed no signs of panic or distress due to asphyxiation or drowning, etc.
>>>Where else would they be?<<<
Maybe they thought they would discover them in the Hunley’s Employee Lounge watching the Super Bowl on the Flatscreen TV.