I mean, think of your own company's PR team. If you've worked for a large company, you've likely had interaction with a PR team that was pretty ignorant about the inner workings of the company. Now, add to that the fact that this is a classified investigation being run by FBI counterintelligence, and interfacing only with cleared employees (none of whom work for the PR team).
Do you release a press release denying everything without asking the guys who are supposed to know about it? Would those guys say to you it's all fabricated and urge you to deny it or will they evade answering it (or even more likely they'll go up the chain)?
This is a CEO level incident.
And as the article describes, the CEOs were summoned to DC, briefed, and at that point almost certainly asked to keep the investigation under wraps.
Apple and Amazon are compelled to lie. It's a classified investigation and likely only cleared employees are aware of it, and they have to deny its existence or stand to lose their clearance (worth $$$).