The answer is kids. Especially with DS games, kids throw out the case and carry the games either lose of in larger travel cases. I've had kids come in with sandwich bags filed with just lose DS games. The same happens with disc based games -- they'll throw out the case and keep it in a binder or just laying around, which is why a good 50% of what I see are covered in random scuffs. Only about 10% of the DS games that come through my store have cases, and those do get thrown out so the cart can be put on display to save space. As for new games with generic art, that's because people steal them, usually thinking the game is actually inside, because they're morons.
In a related story, I once had a kid buy a 360 game and argue that I should just throw out the case because he didn't want it. He absolutely refused to take the case. --- There = location. Their = possession. They're = "they are". Then = time. Than = comparison.