Senko
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I think there is no official answer on the effect on wooden shields/armour. I'd imagine a penalty to the AC benefit from the item would apply. Something similar to the -4 a weapon gets.
As for magic items that's in the rules on damaging magic items I'd say . . .
Damaging Magic Items
A magic item doesn’t need to make a saving throw unless it is unattended, it is specifically targeted by the effect, or its wielder rolls a natural 1 on his save. Magic items should always get a saving throw against spells that might deal damage to them—even against attacks from which a non-magical item would normally get no chance to save. Magic items use the same saving throw bonus for all saves, no matter what the type (Fortitude, Reflex, or Will). A magic item’s saving throw bonus equals 2 + 1/2 its caster level (rounded down). The only exceptions to this are intelligent magic items, which make Will saves based on their own Wisdom scores.
Now that is dealing with "damage" but I'd consider warping its shape as damage even if its not dealing X damage to hp but the spell allows a save to negate anyway. So if you use warp wood on a magic item it'd make a save as detailed above. The spell specifies that will negates so if you used it on a magic item (sword, shield, X) I'd have it make a will save with the above bonus.