The design at the upper sides of the airbox near the subframe spars allows water to enter. As stated, water can also come in through the seams of the airbox. Its not even close to water tight.
In saying that, I often cross water deep enough to change the sound of the engine from bike to boat and find the airbox works quite well. Yes it will take water on, and no the duckbill doesn't drain it nearly fast enough, but it doesn't seem to get pulled through to the engine if a good quality filter oil is used.
I have slit my duckbill open more to allow water out easier, sealed the airbox some more with silicone when new (now 75hrs and a lot probably isnt so sealed anymore), and in addition to that take the time to pull the whole rubber duckbill out when a) washing the bike and b) after crossing a deep river. You'd be surprised how much water can be flowing out of the airbox while the engine continues to run with no signs of water ingress.