It's been pointed out before that in a real-world situation, "checkpoints" in the usual sense would have zero usefulness in space. Here on Earth, you put checkpoints at choke points: places where the geography restricts travel, so that people have to pass through them in order to go someplace else. The only road into or out of town, for example, or at border crossings. In space, there are no roads, and virtually no obstacles that restrict full 3-D movement. If someone establishes a "check point" all you as a visiting pilot have to do to avoid it is to sail around it.
They could give checkpoints some meaning if they wished to, I suppose. When nav beacons were first introduced, they were "useless" too, until FD implemented the scan-the-beacon-for-information thing. Personally, I'd like to see planets and stations in war/civil war/lockdown systems be temporarily permit-locked; if you wish to dock at that faction's stations while the war/lockdown is happening, you'd have to visit a checkpoint to be given a temporary permit, from the faction that controlled that checkpoint. In a war situation, owning a permit from one faction would see you fired upon by military forces of the opposing faction. That might add a bit more danger to flying in a warzone, a sense of "there really is something bad going on around here, that civilians should stay away from". Anarchies, of course, wouldn't be concerned about permits and checkpoints.