1)Where does it say that enhancements are supernatural?
They're magic, and they're not spell-like. That only leaves one thing...
2) Under Magic weapons and Armor, it says "Magic armor bonuses are referred to as enhancement bonus..." and "Magic weapons have enhancement bonuses ranging from +1 to +5."
That's a short form. Magic Armor bonuses should be referred to as enhancement bonuses to armor...
Why would the item lose all its magic? Polymorph Any Object states "A magic item or weapon or other object can be polymorphed into another type of magic object, but it never gains abilities superior to those of the orignal object." Equal is not superior.
A +5 weapon is superior to a +5 suit of armor. A +5 bonus to attack rolls is about equal to a +5 bonus to armor, but there's also the +5 bonus to damage, and the ability to penetrate damage reduction, including
stoneskin (and the +5 armor doesn't grant any sort of damage reduction). That's why the weapon costs twice as much as the armor. Furthermore, there are many types of enhancement bonuses. Not just to armor, attack and damage, but also ability scores, number of actions per round, movement rate, and so forth.
If you were to turn a Gauntlet of Ogre Power into a sword, you don't get a +2 sword
The save is not a big deal, it will fail sooner or later. What would the save be anway, figuring at least a DC 26 for an 8th level spell with a 26 int?
The item has a caster level of at least 15th (for the +5 bonus), so it gets a save of 10 + 1/2 caster level +2, or +19. It would fail more than half of the time.