I just looked into event handlers for explosions, and realized that no event is fired when using World#createExplosion. This means it is very likely that WorldGuard won't be able to protect regions that are struck by explosions from wand projectiles. So if the item set uses explosion projectile effects and a player obtains such a wand, he would be able to destroy protected regions with the explosions.

I should try to cancel explosions that are in or nearby protected regions (or prevent them from breaking blocks). I'm not yet sure what would be the best approach to determine a hit.

This will be fixed (well... mostly) in Custom Items 9.4.