If you know what you're doing(which Apple should since they created the constraint system), then it's not that hard especially with the current constraint structure. There really isn't any technical reason why they shouldn't be able to reimplement iTunes natively and use backend API's to just serve content.
Having played around with apples layout and general UI related stuff myself quite a lot I can tell you that it's a lot harder than webviews. We are talking perhaps 50X for the kind of stuff like the App store.
Apple totally has the resources to make a great native app experience, even if it's much more tedious. I don't see why they don't go the extra mile, especially since the app store generates so much revenue...
This is not a question of ability but what is gained from making it native vs. hybrid. You don't gain anything from using the native layout model that can't be done via web view.
There is no doubt the App Store is horribly done, but for the kind of content that is going to be in the store I simply don't see why they would choose otherwise.
Keep in mind that the apps also exist on the web. This would force apple to still make a web version and a native version.