After 1.0, Handbrake now uses an in-app auto-update feature so you no longer download it from a website. As the article mentioned, anyone using a version prior to 1.0. This malware only occurred if you downloaded Handbrake from the infected mirror site. Yes, many commercial DVDs still use libdvdcss for protection.

This has been known on the Internet ever since Apple started using sandboxing. No hacks are needed and Handbrake will automatically find the library file and decrypt the commercial DVD. The name of the file is 'libdvdcss.2.dylib'. You need to use Pacifist to extract the library file from the installer package to manually install the libdvdcss library file. Installing the libdvdcss file in the /usr/local/lib directory does not interfere with Apple's sandboxing. If you do not have the lib folder in your /usr/local directory, create it.

Then you have to manually install libdvdcss in the /usr/local/lib directory. You have to download libdvdcss separate from VLC, which has been that way long before Apple's sandboxing. Handbrake continues to rip commercial DVDs as long as you have libdvdcss installed, even with macOS Sierra.

Libdvdcss mac