As against the other two branches, all the court has is political capital. Nothing stops the President or Congress from just ignoring a court decision. The judiciary spent tremendous political capital during the civil rights era, and doesn't have enough left to battle the current era of overreaches in the name of national security. And in any case, national security was always one of the areas in which the executive branch was considered to be supreme over the other two branches.
In general, lower courts follow the lead of appellate courts, which in turn follow the lead of the Supreme Court. And on constitutional issues, those justices don't like to get too far out in front of what they believe the national consensus to be. That's why you have toothless rulings like U.S. v. Lopez, a commerce clause case that conservatives initially applauded, only to have Congress slightly tweak the law without complaint from the courts.
Sure, but there is definitely a "mood" in the judiciary. If you read opinions from today versus those in say the 1970's, you can definitely see a self-concious deference to the political branches that didn't exist back then. E.g. compare the D.C. Circuit of the 1960's to the current one.
In reality the DC Circuit spends much of its time today striking down regulations enacted by the political branches, and actually takes some glee in doing so. In HNesque areas, the court tossed out the Net neutrality regulations and the broadcast flag regulations. There's a reason the president wants to tilt the makeup of that court.
Judges should be issuing warrants for searches, and denying them when appropriate. But what if a judge appropriately denies a warrant for an overly broad search with no evidence of wrong doing on the part of those being searched, and then a building is blown up and it turns out the overly broad search would have caught the bastard? The judge acted appropriately, but he'll be crucified none-the-less.
Too many people don't want to take the responsibility for doing the right thing and having bad come of it, so they'd rather do nothing, or even the wrong thing.
The laws that brought NSLs and similar things were designed to make it incredibly difficult and expensive to appeal in a court. The alternative to warrantless searches has been a top secret court dedicated to National Intelligence issues that approves 97% of warrants. The PATRIOT act laws circumvented even that nominal oversight.