The problem with an unscannable cargo hold (if it were possible) is that it is unscannable. It would become a free pass for smugglers, which is not the point. As you can't be boarded and searched in game, the only option available is scanners. Take away the possibility that smugglers can be caught, and you kill the point of the ID.
If people would use legal goods to hide illegal goods, sure.. i'd be more inclined to let em by...
ex: Pharmaceuticals and Cardamine
Mining Equipment and other such items and Artifacts
Maybe even Passengers, VIPs etc and Slaves...
But sad truth is, no one does.
Almost every smuggler I see is fully loaded on illegal goods, something that is impossible to hide when in scanner range.