I give my admins '' as a permission.
It's really silly that I grant them ''
then ungrant them vanish.lightningbarrage, vanish.explosion, and vanish.smoke.
Otherwise, they do all of these effects when they log in / vanish

These should be /v smoke /v lightning and /v explode. That way they can have permission to do it AND pick which one they want to do. /v can be just standard, quiet, effects-less vanish

It is very silly that you give your admins every node when you don't want them to have every node! ^_^

In 3.9 the effects will be toggleable (and remove the on-login bug), but having * will still mean you by default do that when you /vanish. Don't give yourself nodes you don't want.

It's strange, you seem to treat permissions like a configurable system (which it can be), whereas most other plugins devs treat it like privileges with commands separating the different functions.

What do you do for OP only permissions?

There's a set of permission nodes granted to ops. You can see in the plugin.yml