I think the visibility of these dialogs serves as a warning to the user--but they should do a better job directing the user's attention to where the threat is. If the user is getting annoyed at all these pop-ups, he should direct this annoyance at the developer who is (in all likelihood) asking for access to more of the user's computer than he needs.

The fact that there are so many popups should mean apps are reaching for access to your system way beyond what they should be. It shouldn't mean Apple needs to get rid of the pop-ups.