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I think the problem is that you have no iOS experience. Those "bubbled" numbers are called (notification) badges, the informational messages that appear at the top of the screen are called notifications and can also be found in the notification center. IIRC it's the same with Android. Well, Android borrowed the badges, iOS borrowed the notifications.
Personally I don't think these feature should cause any confusing, certainly not on the long term and users prefer to have them.
Neither the badges or the notifications change the icon grid in such a way that people are not able to launch their favorite apps.