Is underwater vision not shape dependent? I don't understand how my con got scouted here, and am quite confident it cost me the game.

What had sonar to detect the conch though, and was in a position to detect it from?

Right.
Sonar ignores terrain.

It is a legacy Spring engine thing.

Radar used to have a big problems on sea maps against surface ships as their coverage would still follow the underwater terrain and be blocked by underwater obstacles even if the target was at sea level.
That seems fixed now.
But sonar has always just went through terrain obstacles in Spring.