I don’t know enough about constitutional law to make a judgement on this statement by the EFF.
Essentially the Government is saying that, even if the Judiciary found the wholesale surveillance program was illegal after reviewing secret evidence in chambers, the Court nevertheless would be powerless to proceed, because the Executive has asserted that the Program, which has been widely reported in every major news outlet, is nevertheless still such a secret that the Judiciary (a co-equal branch under the Constitution) cannot acknowledge its existence by ruling against it. In short, the Government asserts that AT&T and the Executive can break the laws crafted by Congress, and there is nothing the Judiciary can do about it.
However, if it’s anywhere close to being true, we are living with a very scary government. Very scary!!