JSON is a fine format for storing configuration data, and any reasonably structured data. So is XML, protocol buffets, what have you.
JSON is a poor format for humans. For a configuration file that an actual human would edit by hand, and read and try to understand later, JSON is a pain.
Comments are mostly useless in a machine-generated and machine-consumed file. They are indispensable for humans, because they are a link to what machines are not doing.
Nice formatting is useless for a machine-consumed file, because they process a stream of bytes. They are indispensable for humans who recognize text very differently.
This boils down to one thing: config files are source code, and need all the amenities that make source code comfortable for humans.