Well I would think that if the customer, in this case the Australian Signals Directorate, encrypted all data prior to going to AWS, it would be protected from any data mining that Amazon does.
I am sure that the ASD isn’t just posting the information unencrypted on AWS or solely trusting Amazon’s encryption where Amazon also has a copy of the key.
Yes that metadata can exist but can’t that be obscured if AWS isn’t connected to directly?
I think some of the technical details of how the ASD intends to ensure data protection/confidentiality/integrity are omitted for national security reasons.