The SDNY and Second Circuit rejected the defendants' first amendment arguments in the Corley case. That was one of the most upsetting events of that decade for me, but I would insist that the first amendment argument
has been tried, and at least in that context and those courts, it lost.
You might ask how we reconcile this with Bernstein, where the first amendment arguments were doing so well. One answer is that because of the DOJ tactic you mention, Bernstein isn't binding precedent.
I think other answers are about "atmospherics": grad students asserting first amendment rights in software are more sympathetic than hacker journalists, even if both are ultimately pretty antiestablishment. Also, as someone else brought up elsewhere in this thread, the courts are probably more used to seeing government suppression of speech as a first amendment problem than suppression of speech through civil litigation by private parties. For instance, the courts surely hate the idea of "banning books", yet they're happy to issue an injunction against a book if they conclude it's defamatory after a libel trial.
So, we might have been better off if a first amendment challenge to §1201 had been raised for the first time in a criminal prosecution of an academic or mainstream journalist. Which indeed would probably never have happened because the DOJ would have been reluctant to go ahead with it. Everyone in the legal system is interested in picking cases of first impression tactically.
There's still ongoing work to challenge §1201 under the first amendment, but it's not as obvious as you suggest that it will work out.