What's the justification? I'm genuinely curious.
Both of these cells go to the public library and check out books on bombmaking and other mischief. They also ask the librarian, "Hey, have you had any requests for records under the PATRIOT ACT?" If they ever hear a "yes", no matter whether it's them or not, that cell shuts down and moves to another city, and the other cell continues its plot.
Leaking even the one bit of knowledge of whether there was a request for anyone would make the investigation harder, and would allow the terrorists to escape and plot the destruction of our freedom elsewhere.
Now, in the real America, the value of that one bit to an evildoer, when applied to an organization Apple's size, as opposed to the value of that one bit to measure PATRIOT ACT activity as part of government accountability, is a good question to ask.
The library could potentially even give anonymised information that might give reasonable suspicion, eg let us know when someone rents these books together and we'll go get a warrant.
The sad thing is that the west currently has exactly this balance in place, but by pushing too hard everything is going to go underground or overseas. We're losing the exact capabilities we need to fight bad actors, thanks to the NSA's greed and short sightedness.
If you can't talk about a violation of your Constitutional rights, you can't fight it either.
I think many of the people who came up with this stuff know that a lot of it is questionably legal at best. The justification of these gag orders is therefore to hide the prevalence of the questionable behavior, allowing those responsible to continue what they're doing for as long as possible.
It's along the lines of - if we're monitoring a service to catch terrorists or prevent terror attacks, it's counterproductive to alert the terrorists they're being monitored. Furthermore - if the people trust us enough to allow us to monitor these services (which is supposed to follow from there being laws enabling us to monitor these services [a]) then you must also trust us not to abuse the information we gain or to use it in any way that does not serve the interest of national security, so non-terrorists using the service aren't harmed by not knowing they're being monitored.