I too was looking at something similar to this while I was running the wires for the Bofer84 locker mod.
I thought about running the intake to the windsheild grill vent and putting a 1/2 hood scoop over it. That way I can 'SEE' the water entering the intake as I drive through the slop and shut the engine down myself.

The potential problem I see for routing it into the cab is pulling a vaccum in the cab.
Hard doors on, hard top on, windows up and full throttle might result in some ear pain until the floor drain plugs pop inward.

If anything is open - it will not be a problem.

 

yeah i was about to say.....i think you would have to leave at least windows open all the time.....otherwise you might be quickly killing yourself? hahaha i know our jks arent are tight, but i think if it was pulling hard enough, you'd take alot of breathable air and choke yourself or engine out? just thinking out loud.