Impact of super-polynomial extractors on the security of a zero-knowledge proof
The philosophy behind the extractor and knowledge is that if the prover can generate the proof, then it could itself run the extractor. Therefore, if it can prove, then it knows the witness.
If the extractor runs in super polynomial time, then the prover itself cannot run the extractor. Note that if you took this to an extreme, then in exponential time it is always possible to just find the witness. So, any ZK proof can be said to be a proof of knowledge with an exponential-time extractor. But this is meaningless.
Technically, proofs of security of protocols that would use such a zero-knowledge proof of knowledge would break down.