If I was putting it in there, I'd do it to stop water from sloshing around so that it had no choice but to obey gravity. There's little point using that sort of sponge for sound insulation, but it would trap water preventing it from hitting the air filter.
'Preventing' might be too strong a word. "Reducing the chance of" might be a better term, because sure as chickens lay eggs, someone's going to find a storm to drive through that's powerful enough to force water into the air filter no matter how well designed the air box is.