A diff breathers real purpose is to let the axle "breathe" air from thermal expansion (usually caused by water crossings) not keep water or debris out....that is a secondary function...

Without a breather, or if your breather is clogged, the pressure that builds up inside the axle housing will most likely push gear oil past your pinion or axle seals.

I  wouldnt remove or plug the diff breather however my thought is the down section of the breather would prevent water from coming up the tube, when you enter the water the diff will cool rapidily and the inside air and outside air should neutralize then when the rest of the rig enters the water the air in the diff will prevent the flow of water in. 

So that you wouldnt have to worry about plugin the diff breather for crossings, the desighn would allow for free pressure equalization and still protect auto...