Cargo Scanners allow all the contents of a cargo hold to be examined. (This includes items inside containers - regular containers, locked containers and general freight containers used by freighters.)
Using a cargo scanner on a locked container located inside a ship will allow the scanning pilot to see what is inside the locked container. (The contents are still safe from being accessed, you can just see what is inside.)
There is no way to hide the contents of a ship's cargo hold from a pilot using a cargo scanner except under thoses circumstances.
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