Retaliatory Prosecution
Although probable cause should generally defeat a retaliatory arrest claim, a narrow qualification is warranted for circumstances where officers have probable cause to make arrests, but typically exercise their discretion not to do so. In such cases, an unyielding requirement to show the absence of probable cause could pose “a risk that some police officers may exploit the arrest power as a means of suppressing speech.” (Internal citation omitted).
Assuming that standard applies to retaliatory prosecutions as well as retaliatory arrests, then it would be open to Bolton to try to show that whatever he may have done is not the sort of act that would usually result in prosecution. The government could respond to a future motion to dismiss an indictment of Bolton by pointing to the fact that Trump himself was indicted for mishandling and unlawfully retaining classified documents. Thus, the government could argue that the case doesn't fall within the Nieves exception.
To be sure, the prosecution of Trump was dismissed by Judge Aileen Cannon based on her conclusion that Special Counsel Jack Smith's appointment was invalid. I think that ruling was mistaken, but regardless, that doesn't appear to speak to the question whether the prosecution of Bolton fits within the Nieves exception. Smith was duty-bound to apply the Justice Department's ordinary guidelines for prosecution. The fact that he concluded that a prosecution of Trump was warranted undercuts the notion that Bolton would be subject to prosecution for something that does not usually result in prosecution.
But not fatally. Even assuming that the FBI search of Bolton's home and office turns up evidence that he unlawfully retained classified documents or mishandled classified information in some other way, it is quite possible that he did so inadvertently. By contrast, Trump retained classified documents even after having been given opportunities to return them and then appeared to obstruct the investigation. So it's possible that Bolton could show that people whose conduct is more like his than like the blatant law breaking of Trump are rarely prosecuted. That would leave him potentially eligible for the Nieves exception.
However, the Nieves exception might not even apply to selective prosecution cases. In Nieves, the Court distinguished Hartman v. Moore, which was a retaliatory prosecution case. The Court conceptualized its "narrow" exception in retaliatory arrest cases as different from the rule in retaliatory prosecution cases. The latter do not admit of even a narrow exception to the requirement that persons asserting that a prosecution was retaliatory must "show more than the subjective animus of an officer and a subsequent injury; [they] must also prove as a threshold matter that the decision to press charges was objectively unreasonable because it was not supported by probable cause."
But wait. In that last quotation, I inserted the word "they" in brackets where, in the original, the word "plaintiffs" appears. As that indicates, Nieves, Hartman, and just about all of the reported Supreme Court and lower court cases addressing retaliation allegations arose as civil suits. And much of the Court's analysis in those cases is drawn from general pleading and proof practices in civil cases involving claimed violations of civil rights. Perhaps the Nieves exception or some other rule favorable to alleged victims of retaliatory prosecutions does apply after all where the defendant in a criminal case moves to have the prosecution dismissed on the ground that it was brought in retaliation for protected speech.
And indeed there is good reason why the Nieves exception should apply in retaliatory prosecution cases where the issue arises via a motion to dismiss the indictment. The Hartman Court insisted that plaintiffs must show a lack of probable cause to win a retaliatory prosecution claim because of a distinctive feature of civil cases: prosecutors have absolute immunity against civil damages. Thus, a retaliatory prosecution civil claim will necessarily be brought against some government official other than the prosecutor. The obligation to show lack of probable cause is necessary to link the allegedly retaliatory motive of that other government official--typically an arresting police officer--with the prosecutor.
However, where the issue is raised as the basis for a motion to dismiss an indictment, there is no nexus problem. The allegation by someone like Bolton would be that the prosecution as directed by the Trump Justice Department was brought to retaliate against him for his criticisms. Adimittedly, to make out such a basis for dismissal, it would not be enough that Bolton show that Kash Patel was retaliating against him because the FBI is responsible for the investigation and (potential) arrest. Bolton would need to show that Attorney General Pam Bondi and/or other actors in the branch of the Justice Department that made the decision to indict (if and when such a decision will have been made) did so based on a retaliatory motive.
At that point, the Nieves exception ought to apply. It should be enough for Bolton to succeed in having an indictment dismissed for him to show the retaliatory motive and that people similarly situated to him but not in the crosshairs for their speech are typically not prosecuted. Whether the courts, including SCOTUS should the matter come to it, in fact will extend the Nieves exception to such a case remains to be seen.