i have now migrated my notes to Joplin, and (manually) tagged them. Regarding the desktop app i have following suggestions to help improving the tagging system for the desktop app:
making tagging easier
have a line at the bottom of the window (or under the Button-bar) that shows the tags of the current note. In this case you see all tags at one glance while you edit the note.
As a bonus, when you click on a tag, it could have the same effect as clicking on the tag in the left pane - show all notes with this tag.
Middle pane (where all notes are shown): show which notes are already tagged by adding a small icon next to the title. In this case you see if there any notes that are not tagged yet.
I know that maintaining Joplin is a hell of work, so feel free to take this suggestion or drop it since there are more important things to do.