Like jwaller stated, the vents are check valves. When these trucks are operated on highway, the differentials heat, causing the air inside to expand. The breathers keep pressure to a minimum, venting. When a hot axle is submerged, it is suddenly cooled. But since some air was expelled when heated, the pressure in the axles drops. This overwhelms the seals and water enters the bearings from the inner axle seals and also from pinion seals, if you go deep enough.
Yes, the clutch and transmission are pressurized with the deep water fording kit to keep water out. This could be done with the axles BUT it might cause gear oil to bypass the outer wheel bearing seal.