Professor Zoom wrote:
Why would you use a submarine if you didn't submerge? Why not use a boat? Clearly they CHOSE a sub....
In fairness we can only go by what we see onscreen. Comics and novelizations don't really count. Onscreen we never see the sub actually submerge. That said it was an extremely crazy thing for Jones to do if the sub actually had submerged. In the end the main thing Jones accomplished was saving Marion---he realized what was about to happen and convinced her to keep her eyes closed. Without Jones she might have felt compelled to watch what was going on only to be destroyed along with the rest. Sometime later the ark might have been found again, but Marion would likely have been dead. So Jones did in fact save her only not in the expected conventional way.
Old subs of that era were more effective on the surface than submerged if you wanted speed. There's also the matter of fresh air supply. So if you have no reason to be concealed than you stay surfaced. You only submerge if you want to sneak up on someone to attack them or if you're hiding from reconnaissance planes or enemy ships.