I want to rig up a mushroom top for my southdown to eliminate the rain issue. I'm sure the amount of rain that is pulled it prob get pulled through the engine or evaporates out. Not sure but tons of trucks run safari style tops and it doesn't seem to be an issue.

 

First, the drain holes are small, its not going to suck up any water through those holes.
Second the air filter will stop the water from getting past it.
Third, if you stop in water that deep with a petrol engine water in the air box is your last worry.

 

And why would you stop moving?
Did you not walk the water crossing before hand to know how deep it was or if there were obstacles you couldn't see?
Never drive through water unless you know how deep it is and whats under it.

 

Again, raised air intakes are not meant for wading on a petrol engine.
They are for dust control and looks only.

 

Even if it does collect, like you said it'll evaporate once it gets warm.