Will the cargo have a mark, like they do now with smaller boxes?

You will be able to differentiate hauling mission cargo from player-bought commodity cargo. You will be able to differentiate that visually.

Currently, you could do that using a tractor beam, where it will actually give you information about the different kinds of things that you're moving. So you'll have information about the commodity that you're moving, but also it should mention whether it's contracted or not. And then further in the future, we're looking into making that information available with your ship scans as well. So if you're a pirate, you scan a ship. In the future, you should be able to differentiate.

Not just pirates. You could be an escort.

Sure. You should be able to distinguish what cargo is worth taking and what isn't.