There might be a mix up on the details.

The FBI raided the home of John Bolton who was a former National Security Advisor for the first Trump administration. (not directly part of the NSA and definitely not the director of the NSA). Bolton has become a vocal critic of Trump since he was fired in Sept 2019.

Trump's DOJ has a track record of prosecuting Trump's vocal critics. eg. Former FBI director James Comey and New York attorney general Letitia James

https://en.wikipedia.org/wiki/Prosecution_of_John_Bolton

There has been no legal action taken against current NSA director General Joshua M. Rudd or his recent predecessor, William J. Hartman