Wait, what?
No, really, the default assumption is that the monsters are not using any magic equipment at all. Because of that assumption, they get hidden built-in bonuses to compensate. In the unusual cases where a monster actually is using magic equipment (which indeed is lootable by the PCs), we don't want the magic equipment's explicit bonuses to stack with the hidden built-in bonuses. The magic threshold stuff is just a mechanism to prevent that unintended stacking.
Ordinarily, the staff a monster is using with its "thunderstaff" power is really just a staff. The thunder part comes from the monster and his power. It's no different then if you took a staff from a 1st level wizard who was using it as an implement to cast magic missile. The staff won't let you cast magic missile, it's just a staff.
I can see where it would bug you if it worked the way you're imagining... but it really isn't supposed to work that way.