I agree, and thanks to cmort for posting the article link. No way the folks back then could have known about the effect of a blast wave underwater. For their sakes, I hope the theory is true, and that they died very quickly instead of being slowly asphyxiated in the sheet metal tube death-chamber that was the Hunley.
Sometimes when you get to be the first, you also get to be the last.
Conceptually, this is similar to the "compressibility" related crashes of P-38s during WWII. These were caused by control reversals brought on by the phenomenon. As I recall, in most cases, there were no survivors. They were ended by the addition of speed brakes. The fundamental difference was that there were a number of P-38 crashes, at least one survivor of a near crash, and the U.S. government and the aircraft industry looking for a solution.
The odds are, EVERY similar attack would have failed similarly. There was only one Hunley. There were only the C.S.A Navy, and the marginal at best Southern scientific and industrial base to figure out what happened.
The South never got to that point, throwing in the towel after one. A doomed "country" on the ropes militarily and economically isn't going to devote non-existent resources to solving a moot problem.
The only objection I have to the theory is the discussion of the hole in the conning tower. As I recall from previous stories, it wasn't a "bullet" hole, it was more like the hole you'd get from a small caliber cannon or swivel gun of some sort. That would let in enough water to sink the Hunley. On the other hand, the asserted lack of evidence of panic by the crew, if true, would bring that into doubt.