API design matters if anyone outside your app consumes it. Duplicate code makes changes hard and most compilers can't optimize it away. Bad file structure wastes tokens and makes off target edits more common.
These things are important even in a repo with zero human code. A project that's filled with tech debt will always be hard to work with no matter what latest frontier model you're using.
I think a lot of this can be automated with slop detectors that flag messy unreadable code and make agents rewrite it, but you can't say it doesn't matter.