The sys_var class has the deprecation_substitute member to mark the deprecated variables. As it's set the server produces warnings when these variables are used. However, the plugin has no means to utilize that functionality.
So the PLUGIN_VAR_DEPRECATED flag is proposed to set that deprecation_substitute with the empty string. A non-empty string can make the warning more informative, but there's no nice way seen to specify it, and not that needed at the moment.