Or perhaps one point no one has mentioned is that the shock of the explosion travels with more force underwater than through the air. So the boarding hatch could have been warped by the force of the shock wave, and the crew was unable to close it thereby allowing water to flood into the craft. Just a thought.
Good point. Colorado Tanker brought up a point earlier about the crew being found at their post. It's been a while since I wrote that article and I couldn't remember just why I made the assumption that the crew compartment, (people tank) remained dry for some period of time after the boat bottomed out. There are two reasons for thinking this is so. First, had the boat filled with water first, as the bodies decayed, they would have become disarticulated to some greater or lesser extent. Some parts would have been found on the deckplates. Some of the extremities and the crania at least. Secondly, the book I referenced states that as sediment was removed, some stalactites, (not rustcicles, which can form underwater) were found hanging from the overhead. I've not been able to verify this from any other source, but it suggests that the hull remained watertight for quite some time.
Something that runs repeatedly through my mind is the apparent damage to the forward conning tower and hatch. Shortly after the Hunley was found, a generalized map of it's location was published. Of course it was deliberately inaccurate to protect the wreck site, but back in the day, when I was riding the Von Steuben out of Charleston, that was the general area where we tested the anchor! I gotta wonder.