Since the truck wasn't designed to drive in water, I doubt Toyota took anytime to consider totally waterproofing the engine or electronics. That's why it has a hood on it.....
The items that really need to be protected (computer) are inside the cab.
If you find yourself wanting to drive in water a lot - then you're only asking for trouble either immediately (hydrolocking the engine) or down the road (worn out bearings, leaking seals, smelly carpet, electronics corroding, etc).
I don't think there's anyway of totally waterproofing everything....and if you could, is it really worth it? Just stay outta the water!
Like Silverback07 already said.... depending on the terrain, you could easily drop a tire into a hole and you can easily splash water up into the intake at any given moment depending on how you're driving. It only takes a little bit of water to get into ONE cylinder to hydrolock the engine.
If you do stall when fording water...DO NOT TURN THAT KEY!!!