FUBAR has got most of the solution here (I fixed a bug in this code only a couple of days ago so how it works is quite fresh in my mind).
Scanning works like this. If you have a huge ship (destroyer, juggernaut) then you can scan certain subsystems. Otherwise you scan the whole ship. The subsystem scanning flag reverses this behaviour for both types, allowing you to scan subsystems on small ships and an entire huge ship at once.
(When a coder calls a something a toggle it's usually a big clue that the feature has more than one type of behaviour. In coder speak toggle means "What the hell am I going to call this button! It does two different things depending on the circumstances!" Toggle nebula trails is another good example of this.

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So it sounds as though you want to use that flag to make the entire Orion scannable.
Test 2 shows that the subsystem scanning flag actually does the revers of what you think. It makes the whole ship scannable instead of it's subsystems. Still it does not reveal the cargo.
Sounds like a bug to me. It's probably the same incorrect assumption I fixed for the cap-subsys-cargo-known-delay SEXP in a different part of the code. Remind me if you haven't seen this one fixed (or at least commented on/Mantised) by this evening.
EDIT : Okay, it's not a bug. Apparently you can only show cargo on Transports and Cargo. Everything else gets scanned/not scanned
