I use Nextccloud sync in Joplin and every time I changed a file, I got a notiifcation from the Nextcloud client that a file was updated. The same happened at every sync.
Thus I excluded the Joplin directory from the Nextcloud sync client. I’m using Nextcloud sync in Joplin so there’s no reason that the Nextcloud sync client syncs that directory as well.
Unless you use filesystem sync in combination with the Dropbox sync client you can do the same.