I don't think we know enough yet to judge. You have Supermicro saying that they talked to people, including those inside Apple and Amazon, as sources, then you have both companies denying it.

If the story is a plant, then the people inside Apple and Amazon would not be real. Surely even if they weren't going to publish their identities the journalists will do some due diligence to assure they really were talking to employees of those companies?

If the story is true, Apple and Amazon's denials could still be correct. They are talking to spokespeople after all, who have to rely on what they are told when they question people within the company. If the people who know something about it are keeping quiet for whatever reason (maybe they later signed an NDA with the government to get access to additional information, or they put a gag order on them on national security grounds) then the spokesperson reports a categorical denial because they don't have any information to the contrary.

So like I said, we don't know enough to judge either way.