I have had one on my 4runner for over a year. This is a well known problem on Tacoma's since they were one of the first victims to receive the crappy air pumps. Any way below are some pics of the one on my 4Runner never mind the air pumps location it has been moved to make room for a couple of other things. The only thing I have noticed is it makes the pump a bit louder as it probably breaths a bit better now.
With the factory cover on. Not worried about ingesting water on mine the truck will be floating before this thing takes in water on so I will have far greater issues....