What's the different between smart-home-nodejs (https://github.com/actions-on-google/smart-home-nodejs) and actions-on-google-nodejs (https://github.com/actions-on-google/actions-on-google-nodejs) handlers for Smart Home intents? Which method should I use to create a Smart Home Application?
The actions-on-google-nodejs is a library for Node.js which simplifies the work you need to take in developing actions, including smart home actions.
The smart-home-nodejs is a sample project showing you one way to get started quickly with the smart home vertical. It does not use the actions-on-google library, as it was put together before the library supported smart home, and that's an outstanding feature request.
For an example of smart home that does use the library, you can check out the smart home codelab.