Something is just more satisfying when you flatten the Goomba and a little "100" pops up. Like it's the game's way of saying "I approve!" I noticed it when 3D Land all but replaced points with coins. Which is fine, certainly doesn't make the game less fun... but points would've been cool too.
Also I guess it's a tip-off about getting a 1-Up by defeating multiple enemies with one shell/jump. When I was a kid, I would occasionally stomp two or three enemies in a row/kick a shell at a small group in All-Stars, and see the number of points rise with each one. So I wondered how high that number could go. When the opportunity presented itself and I managed to kill enough enemies in a row and was rewarded with an extra life, it was great. Good game design leads you to find things like that without overtly telling you; you still feel like you've uncovered a secret. This was before I had my own copy of World, so I didn't have that really early level with all the red Koopas and an empty shell show me that first...
