Because the NDA was an acting contract. If she was really a black hat she would have burned him just before the election, not a year and a half later.
So do u think Q was telling us about secret missions behind the scenes or that he was saying that to give the appearance that Comey is a black hat? If Comey was that much of a literal threat he would have been neutralized not running a book tour. Not everything can be said 1:1. What makes a good movie?