With the scripting addition List & Record Tools (from one of the Script Debugger developers) it’s possible to delete items in an AppleScript record. Setting a record’s metadata to this changed AppleScript record works (didn’t test with rich text, but it should work too, I think).
My idea now is to delete unwanted metadata from all records in all databases in order to completely remove it from DEVONthink. Would this be sufficient? Is metadata automatically removed from CustomMetaData.plist if there’s no single record that uses it anymore? I really want to get completely rid of it.