"I cannot see the supreme court telling USian 3 letter agencies to forget about obtaining digital data, which will be what this boils down to."
Nope not at all, this boils down to telling them to use existing international treaties to obtain data in any form. Microsoft are fighting this case because as a case law it would give the US carte blanche access to any data without redress and effectively end US tech companies, especially those in the cloud space. Microsoft would prefer to keep its customers in other countries.