If they shouldn't be copyrightable because the world would be better off, interoperability between business is harmed, it is up to congress to change the law. Historically legislation like this harms smaller companies mostly, larger companies can better afford to deal with the requirement to license or the cost/work required to stick to fair use or litigate over it, so the larger companies that can afford to lobby to change the law aren't going to want them changed.
This case certainly sets precedent that API re-implementation can be fair use, not that it always is. Fair use is very fact specific, based on a four part test where having one part in favor can be fair use, and having three parts in your favor can still be infringement. A future case with products that would have a more substantial effect on the market of the original work, or had more of the original work reused than was strictly necessary could very well be infringement. With regards to "the amount and substantiality of the portion used" in this case less than 1% of the original code was copied just measuring the lines of code. Substantiality is harder to put a number on, but arguably it was only a small portion of the original product. This is a very low and for many other APIs a more substantial portion would need to be copied to be useful. The precedential value of this case is unclear without either the law changing, or further litigation.