I think it is reasonably obvious that "pay what you want" can never be 100% literal. Can I pay π dollars? Obviously not. Can I pay negative one trillion? Of course I can't. Can I pay 'what I want' for all reasonable values of 'what'? Yes.
When HB was new, they did exactly this. The minimum $1 has presumably come about because the people who buy at $0.01 are only there fore free stuff - they don't actually want the content, so why make a loss for them?
Edit: In fact, they still do this, and you can get the Mobile or Games bundles for $0.01.
They used to have a 1$ minimum for Steam keys when all their games bundle where also DRM-free. Now that most of the games in the bundles require Steam, I guess 1$ is the de facto minimum.
