I concur with colorado tanker's remarks, the lamp signal was the reason for the open hatch. Also, wildbill, a swell in the estuary or whatever with the very little freeboard on the sub would make a bad combo with the open hatch. I believe I've read that the sub sank twice before in shakedown and whatnot.
Yep, the Hunley sank twice before the Housatonic attack, killing HL Hunley himself. The crew were extraordinarily brave men to sail her knowing the history.