I would just say, that this idea, that each branch of government would be a defender of it's own powers, thus providing a check against tyranny, because it wouldn't want the other branches to usurp its importance, has worked out fairly well. Not across the board by any means, but "ambition to counteract ambition" was one of Hamilton's better ideas.

So you've correctly pointed out the big question? What happens when you ignore the courts? The courts have no purse like Congress to bribe people into compliance and no sword like the executive branch to force it. They can occasionally use the Marshals as an enforcement arm, but it's very rare to have something like FBI vs Marshals.

Ultimately, what Courts have, is this belief in the "rule of law" behind them. The FBI could blow them off for years and years, just like how the FISA court was dicked around with Russiagate, and nothing may come of it like nothing happened to those who lied to the FISA courts, except for FBI lawyers losing their cases, being held in contempt, and the public being shown a litany of wrongdoings.