Here is an interesting conspiracy that managed to remain secret for more than five decades:
https://www.scientificamerican.com/article/confirmed-the-us-census-b/
There were never any whistleblowers even though hundreds of people were probably aware of it.
What this has in common with the Kennedy assassination is both groups of people believed (rightly or wrongly) that they were patriots acting in the national interest.
Very different situations. Government did all kinds of things during WWII using its war powers. If you were told by somebody in authority that the usual procedures had to be ignored because of the national emergency, you did it, and in those days you probably didn’t brood over whether it was right or wrong. Killing a president is something else all together.