Removing the entry in DEVONthink’s preferences does not delete the custom meta data from records.
To delete the actual data from records use Script: Remove some custom meta data.
Script Debugger automatically adds pipes if necessary. But I’m not sure whether in your case DEVONthink also added pipes. Please check if the meta data identifier in DEVONthink’s preferences also has pipes.
Yes, removing an entry from the preferences only removes it from the UI. Don’t know whether it’s the only reason but it’s done for cases where users share a database (if the actual data were deleted from the records then it would be deleted for all users).