Ok, been doing some research on the question of how much powder was in the spar torpedo. I can not find anything definate but the common idea is that there was between 90 to 135 pounds of black powder in the torpedo. The over pressure alone from a explosion of that weight being that close to the boat could have caused some of the plates to spring enough to allow water to enter. Another consideration is the effects of the explosion on the men in the boat, could it have rendered them unconscious? I think possibly so.
As noted in the article on the Hunley the spar was not detactable as first believed, so the boat was not able to plant the torpedo then back away to explode it. I am sure that in the future we will get the skinny on what happened but at the moment it is all speculative.