Nobody here knows how these cases truly work. There's some precedent where you can find gag orders, which make people think that Cook would simply go the "No Comment" route, but to assume those are a blanket procedure for everything is incredibly narrow-minded.

When it comes to National Security, combined with the most valuable company in the US, all assumptions should be off the table. Apple has many reasons to publicly dismiss the claims: their business in China, their marketing as a security-conscious company, etc. They also operate under immense secrecy. Apple has unmarked buildings, top secret projects, a culture of secrecy within the company. They are the type of company that would have innovative approaches when dealing with national security matters.

It would be odd for Tim Cook to knowingly lie about this situation. If definitive proof came out that the chips were bugged and he had knowledge of it, then he could be punished. But, at the same time, if he were able to prove that he lied in the name of National Security, it could be instantly excusable.