Of course Shatter works on it. If unattended, it does not recieve a save. It isn't a magic item, because all magic items must be masterwork. A VoP character's weapons are, for obvious reasons, not masterwork. Besides, being treated as a magical weapon is different from getting enhancement bonuses from a spell, as noted already. If a party is struggling against a deadly enemy on a time limit, will he or she refuse a healing spell because it can be bought (by RAW, anyways) from NPCs for a gold value? Do they refuse protection from a particularly deadly attack mode they haven't gotten protection/immunity from? Will they not try to be as prepared as possible against a villian attempting to end the world? If so, then the VoP player is being an idiot, not Exalted.
I do believe you're imagining the 'buff up the VoP character' problem. Most experienced parties will already buff up before an encounter, and VoP doesn't change that. In fact, it is harder because VoP bonuses already give several bonuses that don't stack with standard buffing spells. Besides which, those are things that can be blasted apart with Dispels, while VoP bonuses cannot.