The following assumes that the subsidiary is incorporated in a jurisdiction other than the US and so is legally an entity of that jurisdiction that happens to be owned by a US company.
Was the data put there by Amazon Inc and retrievable by Amazon Inc?
If so then yes, Amazon Inc can be ordered by the US government to retrieve it.
If not, then the US government would have to ask the subsidiary directly for it or ask whoever is using the subsidiary to hold the data. How whoever they ask responds to that would be determined by the law of wherever the responder is incorporated or located.
There's nothing really special about the cloud in these matters. It works similarly with data stored on paper. If I am in the US and store my papers in a box that I send to a storage company in the US to hold for me the US government could (1) subpoena the documents from me, and I'd have to retrieve them from the storage company and give copies to the US government, or (2) get a search warrant to grab the documents themselves from the storage company.
If instead I pick a storage company that is incorporated and located in another country that eliminates the search warrant option because US search warrants don't apply in that other country.
It doesn't affect the subpoena option because the subpoena is not asking the non-US storage company to do anything. It is just asking a US entity (me) to turn over documents I legally control.