The exhaust may be out of the water when you're riding normally but it's still got water absorbing some of the sound. You also have the bond line itself physically blocking some of the sound. You can tell just from the beach who is running front exhaust and who is running rear.
Sounds aside... If you run your exhaust outlet above the bond line you can expect anything and everything below and behind that outlet to be completely caked with oil and soot. Next think about how you get onto the ski and where you're planning to put that exhaust. Any time you're not on your feet, that exhaust will be right next to your face and blasting right in your ear.