I'm aware that there is the vanish.hooks.dynmap.alwayshidden permission node to hide players permanently, but I think it would be more favorable to have another permission node to make it where players are hidden on the map only when vanished, and appear on it when they aren't.

If you want that, you enable the dynmap hook, otherwise you don't. But yeah, could use some customization there.

So you enabled the dynmap hook in the VNP config?

I have just put on dynmap recently and my users have found out that they can see vanished staff, less than ideal :P Thanks for at least considering though, would be much appreciated if that extra aspect of customization is added in the future.