The mods Coxy, Clogz & JB all completed to the airbox dont alter its ability to collect water, but do increase its ability to ingest air.
If you look at the intake diagram in eLearn, the snorkel off the filter box goes up to headlight level, and having had mine off more than once, while the the snorkel is not clamped and air tight onto the filter box, I fail to see how it is so loose that it could let water in. It is at least tight enough to require some effort to pull off, and holds itself in place.
The lowest point in the intake system is about level with the centre of the wheel hub, so you would have to be going through over 8 inches of water for that to even start to become to be an issue, and that intake filter box is sealed with a flange type design, that while not airtight, is certainly tight enough to keep water out.
So, unless the intake snorkel was hanging off, you would have had to have a wave come up over the bumper to headlight height to get it down the snorkel!!
Its a crying shame that this happened to the OP's car, but as for it being a major design flaw that needs resolving, I am not so sure.