Yes, the plugin will clean up within the frontend site content, which if you deactivate the plugin all these broken shortcodes will come back again, but if you want to completely delete these broken shortcodes from the database, not just frontend content, you should get the Pro version which you have 2 options:
1- if you want to completely delete shortcodes from the database, you will have this option in the Pro version: from Cleaner settings > Advanced > enable this option like this that [ URL: jmp.sh/YXac7eO ] after that, all broken shortcodes will be deleted from the database.
2- if you want just delete broken shortcodes from the backend (dashboard) and want to delete broken shortcodes when saving/updating any new content, you will have this option in the Pro version: [ URL: jmp.sh/5LNPRxJ ] which this option will delete completely after you update post, page…etc so this will delete one by one from the database, but the first option will delete all completely.
And the cleaning will be done automatically, so just activate the plugin and let the cleaner clean up any broken shortcodes for you.