Even if Bloomberg's story is completely true, Apple / Amazon / Super Micro might have no other choice, but to firmly deny it. Because in that case, it's United States vs. China, not just some publisher vs. a few publicly traded companies. When national security interests and international relationships between two largest economies in the world are at stake, it's not Tim Cook or Jeff Bezos, who get to decide, what can be publicly shared, and what cannot.
If the story was true, only a few people in each company would have been aware of these vulnerabilities, and they might not have been allowed to talk to anyone about them by FBI. Then, even if others were informed, they would have to pretend, that they were not.
If it's a national security risk they might not have needed to be compelled to lie at all, but decided to do so themselves. This would be big enough to damage their entire supply chain if they did publicly verify it as truth.
The national security adviser to the president of the United States is the one, who would have to deal with this publicly, if such information was confirmed by some of largest companies in the US. And he might as well prefer to deal with it privately, if it was true.
Not correct. Instead of denying it, they could either confirm it, or non-denial deny it. They would not knowingly issue specific and categorical denials that are lies.
In the cases as this, if you don't firmly deny everything, you basically confirm that it's true. And people responsible for issuing categorical denials might have had no awareness of any vulnerabilities, even if they actually existed.