[If cargo persists in your ship when you despawn and log out,] what happens if you spawn your ship in the hangar? Does the cargo come with it?

That's a great question. No, because, and I'm going to go sit down at my desk and verify this, it's a different spawn process called a persistent cloud. And I'm fairly certain... I need to go double check this right now. It won't have it, but it might actually.

Or people will start accumulating cargo boxes in their hangars.

Well, that's fine, because the hangar itself is only persistent as far as the item ports where you add and remove flair. Loose entity persistence isn't available in the hangar right now. So actually, now that I think about it, I think it will spawn the cargo.