Ah, the Sugar-Boats weren't THAT bad. Underwater performance was actually a little better than the Gatos and they had some success, including the heavy cruiser Kago. I believe more S-boats were lost from running aground than enemy action.
My memory here is thin, and I hope someone with better sources can jump in, but I remember reading US Commanders refer to "Riding the vents" while on patrol. If there was a choice to rely on just the vent valves, it means that there must be bottom valves. Also, without bottom valves, you could not completely blow tanks and keep them empty while underway. Sea action would slop a certain amount of water into the tanks. Also, on a sub, redundant is a good thing. I would think that valves top and bottom would be standard design for any boat.