I reckon it will be fine there Doug. I was smashing around in some pretty deep mud on the weekend - around 900mm judging form the tide mark on the door - and I was cutting back and forwards in it to make progess - the worst case scenario.
I have had a splash of water inside the inlet tube but no water reached the filter.
The old setup I had with the 660cc motor was the same too - no issues.
Here's some photos to show how much crap was getting flung around.


That pour mark on the guard is from mud flowing out of the engine bay, not off the bonnet, so the engine bay was very, very full of water.
The inside of the filter box - sure there's a splash of water in there, but that's not going to hurt anything.

The filter

That's just a dusty mark.