Developers whether be Apple app makers or Cydia app makers use the same Apple developers tools to make them. Therefore follow the same rules as applies to "Sandboxing" apps. Do Cydia apps cause instability problems, yes, especially when people don't pay attention to the iOS compatibility warnings. Do Apple apps cause instabilities, YES. Apps can interact with each other in many ways, so many ways that it is impossible for Apple or anyone else to test for all of the possible permutations that could happen with the hundred of thousands of apps out there. Developers/Programers aren't perfect, they make mistakes, whether iOS, app or hacker, they all do.
Have the bad guys turned their attention to iOS, yes, have they been successful, yes but, not so much, but they eventually will be successfull, at least till apple plugs their exploit. The PDF exploit that Apple just plugged with 4.3.4, was plugged in the jailbreak community before Apple plugged it. Interesting. Apple wages a small war with jailbreak community, but let us face facts, jailbreakers are Apples beta test program and it doesn't cost them a thing. Jailbreak developers develop new apps and spend weeks or months updating them and honing them, and if they are successful, Apple appropriates them and puts them into the latest iOS update. Other words, your are about as likely to have instabilities with Apple app as with jailbreak apps, but jailbreak developers usually respond quicker.
Forgive Tim, his mother must have told him when he was a little boy, that if he didn't behave the "hackers" would get him. He can't help being afraid of hackers.