Nice idea, though I don't think that assigning passwords should be done in add/remove tag dialog. I think it is more appropriate for right-clicking on a tag and choosing "Set Password...". The question here is: what should protected with such tag notes look like in the notes list?

1) I guess by the note's unique ID, which will be acquired with the "Copy note link" command
2) No problem
3) CN will check that there're linked notes and will present choice: delete linked notes as well or replace links with deleted notes' source URL (if any).

This will require splitting the editor into two views: wiki source and rendered result. I'm reluctant to do that.