There has to be SOME sort of breather apparatus. The heat changes inside that axle when you drive, thus the space required by the gear oil and air in the diff changes as well. The breather on my trans was blocked for a while and because of this the trans was pushing oil past the front seal and I had a annoying drip.
There HAS to be something, jack it up, preferable in the middle of the day when you have the most light, crawl under there with a scraper of some sort and you will find something. It's there, I promise. On new quads they are doing whats called an 'accordian' style breather. It is not a 'breather' at all. It is just a little tube with crimping so that it is like a bellow. The tempurature change in a axle is veryvery little if it is operating properly, so this tiny (approx 3-4") bellow is more than up to the job of handling the volume change. This is something you might want to look into for YOUR axles if you drive through water like this. I dont think *I* will put one on because I dont want to spend $5 just to have it clotheslined off by a stick every trip. (I am always 'logging' when I go out wheeling.)
On the front, the rubber plug you saw was very possibly your FILL hole for gear oil, I think my Dakota just has rubber plugs for a fill into the axle. Unless it had a fitting to attach a small hose to aswell I doubt this is your breather, your breather will be at the top of the tube or the diff houseing, so as it see's air and not oil.
Good luck, and have fun learning the underbelly of your truck.