I've never heard it said that anyone was required to deny involvement. Did you mean that exactly as you wrote?
I think there's a world of difference between a gag order where you are not allowed to confirm, and an order to explicitly deny involvement. I'm not saying the former is "good", but there's a difference.
I think there's a non-zero probability that there are US government agencies who can and have compelled people to explicitly deny something that they know is true.
Realistically, it would boggle my mind to discover they'd done that to all the founders/CEOs/legal departments of all the companies involved here (at least Google/Facebook/Apple/Yahoo/AOL), but given the stakes in this game - I have no doubt that it _could_ be done.
I think there's a world of difference between a gag order where you are not allowed to confirm, and an order to explicitly deny involvement. I'm not saying the former is "good", but there's a difference.