I have done something similar, what I call my "selectable underhood snorkle" I cut a hole in the back of the airbox, and ran some 2' plastic plumbing fittings from there up to the top back driver's side of the engine compartment. I used a clean out plug on the airbox end of the fittings. This makes it so I can open or close the snorkle with a quick twist. I cut some sheet steel and made a rubber gasket that blocks the front (stock) intake. This is attached with bolts and wing nuts. It attaches in an open flow and closed flow position.
All this make it so I can can switch between stock, underhood snorkle and a both open configuration in under a minute.
My impressions on the mod are... sweet! I havn't gone swimming with my jeep but with the air intake under the hood I'm sure it would be much harder to suck water into the engine because the new intake is a lot higher, and pushed back away from the bow-wake you get pushing into the water. The underhood snorkle will suck warm air when open, and loose some power due to that, BUT I'm Canadian, and I get some Cold-a$$ winters. If I open both the stock and underhood snorkle openings, my jeep runs better when it is really cold. (warms faster runs smoother) also when both are open I cut down on the intake air resistance and get a noticeable seat of the pants power increase and quicker throttle response.
All in all it cost me about 10$ canadian (or about 1.50$ US) and the only thing I cut on the jeep was the hole in the airbox. Definately worth it.
(would post pics but I don't know how)
Bones