It is, but the possibility of such bugs is a downside to the approach (not saying it's a showstopper but it is a negative). Some of the nastiest software problems to track down are the ones that cause some fundamental assumption everything rests on (often a cache keying assumption!) to be broken, making everything behave wrong, including the tools you're supposed to use to track down problems.

If you're going to build an entire system on an assumption of referential transparency you want to be able to guarantee that everything really is referentially transparent, and one valid criticism of nix is that it can't really enforce that in all cases.