Exactly. The second amendment is arguable. Depending on how you interpret it, it may or may not have been intended to apply to random people having weapons for their own personal protection. Therefore, it is at least possible to argue that the mere existence of police departments, national guard units, and the military are well-regulated militias, and that nobody outside of those organizations has a right to bear arms. I'm not sure I necessarily agree with that interpretation, but it is at least possible for a rational person to argue that interpretation of the second amendment without looking insane or idiotic.
By contrast, there's no way to interpret the first amendment in a way that gives the government any right to pass laws that cause prior restraint of speech of any kind. With that said, courts have generally ruled that certain limitations on speech (as opposed to outright bans) may be allowed if they qualify as "reasonable time, place, and manner restrictions." For example, the government can legitimately say that no protests may occur within two blocks of a cemetery, that no stores can sell alcohol within three blocks of any elementary school, or that no protests can use a megaphone between 10:00 PM and 7:00 AM.
A national security letter's prohibition on disclosure, so long as it is time-bounded, might legitimately fall into that category. If those gag orders have such a time bound, the EFF may have a very difficult time arguing the case (unless the time bound is long enough to be seen by most people as unreasonable). With that said, I'm not under the impression that NSL gag orders have any set date on which the embargo is automatically lifted. If that is the case, then such prior restraint is clearly and unequivocally an egregious violation of the first amendment that cannot possibly be justified under any remotely plausible interpretation of the Constitution or its amendments.
Of course, the fundamental problem is that most people taking an oath to uphold the Constitution against all threats, both foreign and domestic, automatically assume that this means protecting the United States against its enemies, never even considering the possibility that the actions they take in doing so represent an even bigger threat. Throughout history, nearly all of the worst atrocities have been under the guise of protecting the people from its enemies, from the Crusades to the Holocaust. Worse, most such horrors often start out in a manner that seems benign—Hitler and McCarthy, for example—and get progressively worse. National security letters might start out benign, with the best of intentions, but they have the potential for nearly unlimited amounts of abuse, which is why IMO they must be found unconstitutional sooner rather than later.
To that, I would add one more point—that the first amendment is by far the single most important amendment to the Constitution, without which the rest of the amendments are moot—the condicio sine qua non, if you will. It represents the very core of our freedoms. Without the ability to talk about and expose abuses, there is no way to prevent them. Without the ability to criticize the government, there is no way to change it. Without knowledge of what government is doing, the entire notion of democracy—rule by the people—becomes untenable. It is a near certainty that any such government will rapidly devolve into a thinly veiled plutocracy or aristocracy, because the people cannot adequately evaluate their lawmakers in the absence of any understanding of what those lawmakers are doing. For this reason, the first amendment must be defended at any cost, above all other amendments. And that is what the ninth circuit must bear in mind as they make their decision on this matter.