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...
My diff breather is hooked up all the time...its just a hose with a small fuel filter on it. I just keep my filter above the air intake under the hood....if I have water that high I have other problems!