Sounds like the weakness which allows access is in the in-flight entertainment system, so unless you have one of those the threat is probably N/A to cargo.

It would be much harder to access any systems via the external SATCOM link...you'd have to be able to duplicate the signal from the satellite and all it's protocols. Not to mention that the real satellite would still be talking. Could the NSA do it? Maybe. AQAP? No.