Not bold, simply logical
Bloomberg charges a LOT of money to traders for their information, including early access to their stories. They aren't going to risk a multi billion dollar business on a story they aren't 100% confident in. That doesn't mean they can't get fooled if the CIA threw its full weight behind trying to fool them, but I think it is more likely that Apple and Amazon's denials are either wrong or were somehow coerced.
Most likely wrong - if only a few people in each company learned of the issue before contacting the FBI, and they were then told not to tell anyone else, yesterday's denials are easily explained. Press contacts Apple / Amazon spokesperson for comment. They contact various executives asking "do we have any comment on this story" and the executives all know nothing about it and neither do their underlings they talk to - because the odds of finding the three or four people who do know about it are tiny - so the spokesperson reports back that the story is false.
The employees who apparently went to the press (perhaps they were worried other US companies without their resources would be unknowing victims if the government kept the story hush hush forever) aren't likely to fess up to others in their company now - because it would be obvious they had leaked info to the press about it and the company would think "if you leak this, you might leak other stuff, so here's your severance package goodbye"