I read that article also, and when someone has the balls to put their acura NSX's cold air intake into a fish tank full of water, I'm going to trust them. With the bypass I do not see any way that enough water could get into your engine to damage it.
Also, as LoOkN4 said, how would it create a loss of power? I don't see any way that it could.
But, to save money I agree with the other guys that said chop off 1/4 inch of the piping and switch from CAI to shortram whenever necessary.