Well, I haven't done deep water on the Ninja but you could fab a splash shield pretty easily. I ran my 950SE and SMR with pods and lots of rain and a few very deep water crossings in one flooded enduro, no problem. The intakes on those bikes are very high though.
The intake height on this engine/DRZ frame should be as good as a Husky 610, and probably better than my air box on my EXC530, which is just a pretty face. It is as effective as a gill net for keeping water off the filter.
How about running the intake thru tubes to a remote single pod in the stock DRZ box if you are really worried? Hey, if you want to get crazy, fuel in the subframe, air filter up where the tank should be a-la Husaberg-ish. Weld aluminum panels to box in the sub, maybe hang a remote side panel fuel tank like the ones for the older KTM EXCs? Dakar style rear tank? Chop the DRZ tank for an air box?