I helped a buddy of mine with a 2000 GT install one a few months back, the filter does sit pretty low.
He lives in Minneapolis and a few weeks ago when Minnesota had all that flooding he hydrolocked the engine. The car is currently at the Mazda dealership in Minneapolis getting the engine replaced (his insurance is covering it less a $500 deductable.) Why a Mazda dealership? The Ford dealers were backed up with service I guess.
I asked him how deep the water was and he said about 3"-4" or so and he was going about 5-10mph. The car stalled out and wouldn't start when it happened.
His car is stock height, no lowering springs or anything. He and I both were very suprised it could happen in that little amount of water, but it did.