It depends on what you want to achieve with hiding a setting!?
If you want to prevent someone changing it, you should put it into
local.protected.php (
http://wiki.splitbrain.org/plugin:config?s[]=local.protected).
If you want to really hide the info because you would not want anyone to know what the setting is (eg. for security reasons), your approach (removing it from
config.metadata.php) is the best. (You could also hide it by CSS, but that is not really secure.)