You're absolutely right! It's unquestionably the job of the US intelligence apparatus to help secure American interests.
With that said, Apple is a multi-national company, with millions of units used by people of all nationalities. And a vast amount of American military superiority is based on superior technical intelligence.
A carrier group can solve, at great expense in blood and treasure, a problem that intelligence can often solve more quickly and at an earlier point in time. With that in mind, it seems reckless to not take seriously the value of intelligence.
Again, you're completely correct in every way. Apple is an American company! It's just perhaps possible that there could be a bit of subtlety to this.