The first count is "or any restricted data", not classified material. A technological restriction, is enough.
"Knowingly accessed" has never meant you personally. Operators of a botnet don't know directly what they access. They know that the autonomous software is built to access restricted things.
I don't think so:
> or any restricted data, as defined in paragraph y. of section 11 of the Atomic Energy Act of 1954, with the intent or reason to believe that such information so obtained is to be used to the injury of the United States, or to the advantage of any foreign nation
Well I suppose no one has ever been charged under that paragraph of the law then. And the courts have never interpreted it that way.
I understand it was applied in the case of leaking classified CIA material to WikiLeaks, where a former CIA software engineer was sentenced to 40 years in prison.