As far as hydrolock goes, the phrase "...too much water..." may be applicable, but it wouldn't take much water mist on the heated element of a hot wire/film mass air flow sensor to cause it to give a false reading on the high side. Would the resulting overly rich condition cause the Scooby Sport exhaust to sound louder? I'm not sure, but it could certainly cause other problems. <<EDIT: I guess excessive amounts of unburnt fuel reaching one of the hot cats could result in some strange sounds. Especially if that particular exhaust was designed to accentuate certain frequencies. japps - Were the sounds you heard anything like a backfire or popping sound?>>
As far as stock versus aftermarket intakes go, I would say the stock set-up is at least as likely to ingest water, if not more so, than. Quite a few of the aftermarket units, that I have seen pictures of, replace the stock air filter box with a cone filter. That cone filter draws it's air from under the hood as oppose to the stock set-up that draws air in from up front by the grill.
On my completely stock WRX wagon, I've had three "rain events" where I've had hesitation like symptoms. Each event occured under full throttle acceleration, while it was raining, and with in a few minutes of starting the car up after it had been sitting out in reasonably heavy rain. One of the events threw a P0103 DTC.