Answer
This is a known, long-standing bug specifically in the Tool Navigator's display (not a recent regression, and not related to how the files were generated) — the generated implementation files exist and deploy correctly, they just don't render properly in the standard Tool Navigator tree view. The working alternative developers have used is the Favorites navigator instead: add the relevant entity to 'Add to Favorite,' and the generated implementation files display correctly there even though they don't show up right in the regular Tool Navigator.