I think that, unless you actually go into a puddle big enough to get the top of the cowl underwater, any water that would go into the air intake from the cowl would be stopped by the air filter before going into the engine.
About a year ago now, I was off-roading my truck and went through a big puddle...and, on the other side of the puddle, my truck was smoking horribly and barely able to idle. I shut the engine down, took a look to see if something was obviously wrong, and then started it back up, and the engine ran just fine. After getting home, I opened up the air cleaner assembly and saw quite a bit of evidence that water had gotten into the air box (actually, without a drain drilled into the bottom, some of the water was still there; looked like the rest had gone back out the air intake after I shut the engine down). However, on the other side of the air filter, everything looked perfectly fine...no mud streaks or anything on those lines like there was on the "dirty side". I would imagine that FAR more than a teaspoonful of water got into the air intake.
I also did a compression test after this (I was in a state of near-panic, thinking I had bent a rod or 8), and the engine got a clean bill of health. Over 300 PSI in every cylinder (numbers ranged from 320 to 380), and that test was conducted with a cold engine and a weak starter (that I replaced shortly after doing this).
I'm not trying to say that getting a bunch of water into the air intake on a regular basis is a good idea by any stretch of the imagination, but as long as the air filter is sealing well and there aren't any holes in it or anything like that, a little bit of water getting into the air intake isn't the end of the world.
As to the cowl induction, I would love to see some reports of how happy people are with it after long-term use (power, EGT, boost, response, etc as compared to the same setup pre-cowl induction) before hacking into my firewall myself. But, for less than $70, it sounds like a good deal...and better than sucking in a large amount of splash water from the front if you're going through mud and standing water