I don’t know much about Module Builder, but it not obvious to me that deploying a module should include deploying logic hooks. They’re separate issues.
You can build a package for module loader with your logic hooks and other bits of custom code. But often it’s easier to just copy the files over.
If you manage the server, I would advise a simple file copy; if you need your customers to do the deployment of your code, then it’s nice to make a package.