When turning an interactive ZK proof into a non-interactive zero-knowledge argument with the Fiat-Shamir transform, the following security issues must be taken into consideration:
- Even if the interactive ZK proof is a proof system (meaning that it is statistically sound), the Fiat-Shamir transform produces an argument system (where soundness is only computational). In concrete terms, that means that you must in general increase the soundness error of the interactive protocol before making it non interactive. Consider for example an interactive protocol where a cheater has probability at most $2^{-40}$ of producing a convincing proof for an incorrect statement: this can be a perfectly fine security guarantee in many real-world situation. But as soon as you turn this protocol into a NIZK with Fiat-Shamir, the guarantee changes: now, you are only guaranteed that forging an incorrect proofs will take $2^{40}$ computation steps for the malicious prover. But performing $2^{40}$ operations is trivial on any standard computer, hence the scheme would be completely broken. Put differently, a NIZK will in general need to be less efficient than the corresponding interactive ZK proof, in terms of communication and computation, to achieve a sufficient security level.
- Many interactive ZK proofs naturally satisfy non-transferability: if a prover interacts with a verifier and demonstrates that he knows some value, or that some statement is true, the verifier, even after seeing the proof from the prover, cannot in turn convince another party that he knows the value/that the statement is true. This is because the verifier can at best show the transcript to this other party, but by the zero-knowledge property of the protocol, this transcript could in fact have been generated easily without knowing whether the proof is true (put otherwise: if you know the challenge in advance, it's easy to forge a proof. How could the other party know that the verifier had not colluded with the prover and given him the challenge in advance?). In contrast, NIZKs are naturally transferable, since they are publicly verifiable. Sometimes, non-transferability is crucial: suppose you solve a million-dollar problem, and want to prove to someone that you've found the solution. Using a zero-knowledge proof allows you to convince him that you know the solution without revealing it; but you still do not want this person to be able to use your zero-knowledge proof to convince someone else that he knows the solution, since he could then just use your proof to claim the million dollar prize!
- As pointed out by Martin Kromm, the Fiat-Shamir transform is not proven secure in the standard model under any known security assumption. It is only proven secure in an idealized model, meaning that the security guarantees it gives are, at best, heuristic indications that breaking it requires doing "something non trivial" with the underlying hash function. Concretely, NIZKs obtained with the Fiat-Shamir transform have never been broken as of today and seem relatively safe, but we have no proof of that, so one should be cautious.
As for the reasons to use interactive proofs over non-interactive proofs (besides the one above, that apply specifically to Fiat-Shamir): If you want an extremely efficient proof, where verification is super fast and the communication is very small, then this can be achieved using an interactive proof using standard and well studied assumption, such as collision-resistant hash functions (this paper), the discrete logarithm problem (this paper), etc. In contrast, if you want such an efficient NIZK, you either only have security in the random oracle model (using Fiat-Shamir), or must rely on exotic and poorly understood assumptions, such as the knowledge-of-exponent assumption.
As for complexity-theoretic discussions on NIZKs versus ZK proofs, I discussed the complexity-theoretic questions related to the round complexity of zero-knowledge proofs in this answer. There is also some discussion on the hardness of building NIZKs from standard assumptions (compared to the relative easiness of building interactive ZK from standard assumptions) in the introduction of my recent paper, which you might find relevant.