Bugs are filed on GitHub, either https://github.com/juju/charm-tools (for the build portions) or https://github.com/juju/charmstore-client (for the store interactions).
The hooks are generated from the hooks/hook.template file, such as the one provided by layer:basic, or, for Kubernetes charms, the one provided by layer:caas-base. Is your charm or one of the layers that you’re including overriding that file somehow? If the file was missing entirely, you should received a build error, so it sounds like it’s being replaced by an empty file at some point.