How will customs and other checks work when you go to a planet if you have illegal cargo?

You don't want to take illegal cargo to some places. That's probably a bad idea. That's the correct answer in some cases, which is just don't do that. But not only can your ship be scanned in space, but when you land, customs, yes, they're scanning your cargo while your ship's sitting there. They're checking you for weapons. You saw the demo. That's what's going to happen. If you're a bad person, they're not going to let you carry weapons around in cities, at least some of them. And if you're carrying contraband, well, hide it really well. Good luck.