Surely the ability to access the files is irrelevant, it should be about the ability to access the files /legally/. Just because I'm an employee of a company doesn't mean I can look at any file (e.g. network admins being capable of accessing HR files but not being permitted to do so).
Microsoft US (one company) accessing Microsoft Ireland (another company)'s computer network specifically for the purposes of bringing customer data out of the EU- and then specifically so as to avoid having to follow established (and not that onerous for legitimate needs) EU procedures- would surely be illegal.
Indeed, should the very existence of this case not mean that Microsoft Ireland has to restrict access to their US counterparts? This is a blatant attempt to gain unauthorised entry to a computer system, and allowing this would make MS-Ireland criminals in their local jurisdictions as they would be exposing /all/ of their customer's data to the US. It should be treated as any other outside entity attempting to gain access.
Even if some theoretical weakness remained in the system, "You should exploit this weakness, and also you're not allowed to fix this weakness" is a seriously different argument to "the file is there and easily accessible, go get it"