Earlier quoted context omitted.
Thomas's dissent explicitly points this out. Without diving into "are APIs copyrightable?", the majority are skipping what should have been evaluated first before saying if they were fair-use or not.
Why should it have been evaluated first? I understand the intuition you're getting at: logically, the first question could make the second irrelevant. But if the second question resolves the issue even when the first is construed in favor of the other party, what's the rationale for demanding the court focus on the first question?
The main influence of the Supreme Court is in setting precedent. In the absence of a ruling from the Supreme Court, the previous ruling from the Court of Appeals for the Federal Circuit is binding precedent on the whole country that APIs are copyrightable. That means that the most important precedents set in this case are still an issue for the software industry.