A supersonic airplane has a smooth deceleration to subsonic then to landing speed. I imagine the transition from supersonic to full stop in a submarine would be severe. As soon as you lose the supercavitation effect, that water is gonna catch hold and slow you down in a hurry.
Not even supersonic speeds are required for this to be a big issue. Imagine ... you've managed to get the submarine up to, say 300kph or so, and are cruising along just fine. Now, let's say you need to slow down to return to port or a duty station. Making that transition from supercavitation to 'normal' underwater would be a stone bitch! Water is hard.