Did any of the ships in the vicinity responding to the sinking of the Housatonic (sp?)report a collision with anything?
For that matter, a little higher seas or their wake could be just as deadly to a vessel with little freeboard if the hatch was open.
Some of the accounts suggest that after firing on something in the water, one of the blockading vessels rammed an object.
The Hunley was only completely submerged when attacking. At all other times she would have been running with her crude conning tower exposed. If sea condtions permitted she might have had her hatch open. 1 of the theories prior to her discovery was that she was rammed while the hatch was open & that this caused sufficient flooding to send her to the bottom.
All of these theories are subject to revision now that the sub has been found & is undergoing preservation.