Yeah, like merc says, if you have "duds" enabled in the game, they might also run deep, but to your question, going deep and shallow would probably make the "collision detection" place in another damage zone, so I could see that making a difference. There are all sorts of ways to "target" a ship. Read through Rockin Robbin's
Sub Skipper's Bag of Tricks thread and watch some of the videos there.