Charlie, I am sympathetic to most of your argument. But the law has never been that “If there’s not enough evidence to put out a warrant for somebody’s arrest, there’s not enough to take away his inalienable rights.”
The principles at work here are due process and reasonable search and seizure (the Fifth and Fourth Amendments, respectively). These are not fixed terms; what they require varies based on the circumstances. To arrest a person for a crime, the government has to have probable cause; but if it only wants to detain temporarily (and “temporary” can go on for a while) it only needs reasonable suspicion. If the government agents want to search your home or tap your phone, they don’t necessarily need probable cause that a crime has been (or is being) committed. If it is a national security investigation they merely need probable cause that you are an agent of a foreign power (which could be a country or a terrorist organization).
There is question, moreover, about whether the Constitution even requires such a showing. Prior to 1978, the courts had no formal role at all in permitting national security surveillance. (That changed with the Foreign Intelligence Surveillance Act — FISA.) Intelligence gathering against foreign threats to national security was deemed to be within the constitutional purview of the executive branch, with no warrant requirement or judicial oversight. There remains controversy about how much unilateral authority the president still has (see, e.g., the debate over the NSA’s Bush-era warrantless surveillance program). Both the Carter administration (in agreeing to FISA for conducting national security wiretaps) and the Clinton administration (in agreeing to extend FISA to physical searches) took pains to qualify that the president’s signing of legislation that prescribed judicial oversight did not and could not eviscerate the president’s inherent constitutional authority to act without judicial permission in appropriate cases.
The reason governmental authority cannot be set in stone in this area is straightforward. The Fourth Amendment says searches and seizures (including arrest) have to be reasonable. What is unreasonable in some contexts is reasonable in others. In criminal investigations, if the police arrest or search without probable cause, that is presumptively unreasonable. But that is not the case in other contexts. The Supreme Court permits “special needs” searches on less than probable cause in various situations (e.g., drug screening for public school teachers, warrantless searches of people on probation, etc.). The principle was explained by Justice Scalia in Griffin v. Wisconsin (1987).
National security is, of course, the most compelling of special needs. The government is thus given a wide berth when there is a legitimate connection between a precautionary measure it wants to take and public safety – a berth that gets even wider in times or war and other emergencies. This does not mean due process disappears. It means the process that is due is less robust because the desire to search or seize is reasonable under the circumstances.
It remains true, however, that due process can never be illusory, since that would mean no process at all. At a minimum, due process requires a meaningful opportunity to be heard in opposition to a government security measure that has or may deprive one of his fundamental rights. (Due process also generally requires notice of what the government wants to do, but, again, context matters: prior notice is not required in many situations that implicate national security, or even in ordinary criminal investigations – the government does not have to give you notice that it wants to tap your phone; the courts permit notice after-the-fact.)
As both you and Jonah point out, there are substantial arguments that the opportunity to be heard in opposition to having one’s name on the watch list and no-fly list are inadequate. See, e.g., “Terrorist Databases and the No Fly List: Procedural Due Process and Hurdles to Litigation” (Congressional Research Service, April 2, 2015).