So I'm imagining a bunch of Java classes loaded into memory. They're objects, and they have methods, and those methods refer to methods in other objects. Creating this state of memory is functional, and definitely not protect-able. Now, the interface declarations, then, are just a description of this state of memory. A method has a particular name or a particular set of parameters but those are just a description of the functionality, and there is no other way to precisely describe that state of affairs. The closest analogue I can think of to an API is a phone book, and the names and addresses in a phone book are not copyrightable, although higher-level structure might be.
I think the court got stuck on the verbatim copying and that prevented them from seeing things this way.
And even if they were, if the originals were copyrightable, there's no copyright-relevant difference between "typing them themselves" and "copy and pasting", both are verbatim copying (and, even not doing a verbatim copy and merely doing a "derivative work" based on the existing API would be -- barring fair use or other explicit exception -- a violation of copyright if the API, as such, was copyrightable.)