Hello, I've tried disabling effects and silent join on my admin group:
admin:
permissions:
- '*'
- -vanish.effects.smoke
- -vanish.effects.explode
- -vanish.effects.lightning
- -vanish.silentjoin
- -vanish.silentquit
But even with these negative nodes, I'm joining vanished and triggering all the effects :(

Try asking for help at your permissions plugin's page. Though you might wanna try moving the * node below the others.

What ammar said