I don't know anything, but to me, it seems that one in the side might actually drain better? I can also see where it would be more noisy though.
The reason i say that, is because a hole in the bottom NEVER gets any air in it, its just gravity-fed. Right? If that is correct, I would think it might be a little slower draining, which again, may be a better thing, I really don't know how much flow you need! :p