Just to clarify, it doesn't really matter if we're talking about perms or other items.
If you give someone item permissions, it means you trust them to take
anything.
Essentially, before giving someone ANY item permission or filling the storehouse, Kage and vice(and anyone donating to storehouse) should always ask themselves what's the worst ten/twenty things that could possibly get taken in a single looting spree.
If ten Super Potions go missing, will people get butthurt? Probably, so why risk it? Runes, oils, and loads of other crap can be taken by anyone with basic storehouse privileges.
Essentially, if someone gets robbed/tricked because he trusted other people to be nice people,
he should've known better. Tough and unfair, but there it is.
Now, what can be done about it?
1. Closed storehouse. Keep stuff inside if you want, and only leader gets privileges. If someone needs something, they can ask nicely for it.
2. No storehouse. Tradescreen everything.
3. Only village with people you can trust. You can trust them when they know you know where they live, and how far you're willing to go to get even.
These options, are of course, for extreme circumstances where you need to assume you're filled with a village full of kleptos and other asshats.
The easiest thing to do in an average village is to selectively shut down item privileges based on senority or something, and never let people loot more than three or four things per day. If they need more, they can ask.