Really? What tests?
If you lob a Tenere in a river or a large puddle, water will get in through the normal (stage 2?) filter. Trust me, I've tested this ;-), and you've said the same. An air filter that was waterproof would be pretty rubbish at flowing air. Besides, anyone that's had a DNA filter long enough to need to clean and re-oil it knows that when you run it under a tap, there's no real resistance to waterflow.
The stage three filter is made of the same stuff, so water will flow through just as well. The difference is that it will do so when wading if the water gets to the bottom of the airbox, rather than the top. The wading depth of the bike is relatively poor anyway compared to the likes of the 690 and the BMW 650s, why make it worse?
Additionally, and even if you don't go through standing water that deep, it's taking the full force of any water and mud that splashes up. You might argue that the S3 filter means water will drain out as well as in, but water going through the filter is going to degrade the filter oil quicker, and mud coating the outside of the filter is going to stop it breathing well anyway.
Even a small amount of water in the bottom of the airbox - not enough to get sucked into the cylinder - will end up draining into the cases via the breather, degrading the engine oil and reducing the life of the internals.
So no, I don't think the S3 filter, wonderful as the airflow through it may be, has any place on a bike that gets used in the dirt.
Oh and who actually does this? Well, the video below is a public road in Wales that quite a few on here will have ridden down...
http://vimeo.com/51813348