If you go over the wave, half your ship ends up cantilevered over the peak. A ship isn't built to hold half its weight in the air like that. It will break.
If you go through the wave, the upper decks get hit by a wall of water. The windows blow out, the bridge is destroyed, the computers are toast and the ship is swamped.
The wave drag (or wave resistance, to disambiguate from the shock wave drag of supersonic aerodynamics) referenced in sibling comment is the energy contained in the waves created by a surface vessel. The details that you'd have to understand to optimize a hill shape are quite complicated, but for a simple surface vs sub comparison it's enough to know that surface waves exist and that they contain energy that is projected away. A sufficiently submerged vessel does not create those.