I don't want to mix up the side issue of "should code-based research always provide source code" with the metaphors being discussed. I definitely think useful CS research can happen without source code needing to exist, which I hope is the NuPRL project's case.
I do feel code based research should provide source code that was created as part of the research when it is material to their claims, including 'we ran a simulation' and similar findings. If you already have that level of detail, you should include it. If you make claims based on data, you need to provide that data. If you make claims based on source code, you need to provide that source code.