Based on where it was found I recall it was concluded that they sank on their return trip when they lost bouyancy from water coming in the hatch while they were signaling. (?)
I went to see the Hunley in Charleston. It’s a little hard to find on this huge naval base, but it is well worth the effort. There is a cut away model of the Hunley, and the first thing you notice is how absolutely cramped it was, and how it would be impossible for anyone but the lookout to escape through the tiny hatch in an emergency. Just to leave the submarine in normal unhurried circumstance would require careful coordination of the crew and no small amount of gymnastics. The mystery is why there was no sign that the crew had ever moved from their places, or any evidence of an attempt to escape. Next, it was interesting to see that the “ballast tank” was simply an open pool of water uncontained on the top with a front and rear partition rising maybe three feet from the bilge.