The NDA isn't the only reason you don't risk interference in an ongoing investigation though so regardless the basic point still stands.

Even in the absence of NDA, are you allowed to? Counsel has apparently advised them not to. Would it not carry the risk of being complicit to a crime?

Perhaps there is no NDA on the fact that subpoenas were issued, but still an NDA on whom they were issued about? Limiting The scope of such an NDA feels like a plausible result of negotiations after a motion to squash the subpoena.