Yes, there is.
For no-rest zones, it is a mechanical way of representing that there is simply too much going on in the area or the area itself is disturbed in such a way that would prevent resting with any benefits. In the case of Krandor Crypts, there's generally too much unrest or "bad mojo" or whatever you might call it for one to get rest. The hairs on the back of your neck stand up, you get this very uneasy feeling or any number of other things that keep you from truly resting.
As for no-magic zones (and wild magic zones as well), yes, there are reasons for those as well. Part of the answer lies in what those zones are in an IC sense. That little bit of information is only known to a few, but a suitable IC answer is that the Al'Noth in such places has been damaged or distorted in some significant and extreme way.
OOCly, both are used as a form of game balance. They increase the challenge level in a particular way, requiring a different sort of tactic to overcome them. In particular they require either a conservation of spells or figuring out a way to not need the spells at all.
