Currently I have no idea how to turn it off when you are an OP or when you have the * permission.

Note: Using PermissionsEx
Giving my moderators the permission -vanish.effects.toggle.lightning does work, no lightning is produced. But my administrators have the node * to get everything, and when using this, the -vanish.effects.toggle.lightning seems to be ignored!

I could always just write the plugins all permission in case it's needed, but if it's possible to fix it so that the negation also works when you use the * node

It is never enabled with OP. It is enabled with the * node.

Imagine a pizzeria.

You order a pizza with "Everything on it" and are given a pizza with all the toppings. This is OP.

You order a pizza with "Everything on it" and are given a pizza with all the toppings, some paint chips, dirt, and someone's finger. This is the * node. It is op, plus things that nobody thinks should be included in "everything."

So, remove the * node and grant op and you're fine.