I bet the carriers are interested in app updates happening over WiFi and through syncing with the desktop. They would rather someone else foot the bill for that bandwidth.

Most of my apps are tiny in comparison to the actual amount of data (map tiles, images, youtube vids, web pages, etc) that I download. Streaming music is another big drain. I don't think the apps are even a rounding error in the whole bandwidth picture.

Most carriers have enough network capacity to not really care. It's just AT&T that doesn't have a decent 3G network; Sprint, Verizon, and T-Mobile are fine.