Vermin are not the cause of bones and shells disappearing, I believe; it is rather the fact that anything in a refuse-enabled stockpile will wear away over time.
I've read the exact opposite somewhere in the forums. is there proof for either version?
@TruePikachu: aboot ur [x Log x] item, if u give some time to check ze DFwiki, after 10 bites from a vermin any item gets it quality lowered by -1
Normal => x *** x => xX *** Xx => Destroyed
Easy ways to test these:
1) Place a stockpile under some random, normally-nondeteriorating items (say, stone furniture) and in the settings Enable refuse, but Block all of it. It will still count as a "Refuse" stockpile but nothing should be brought into it, leaving your control group alone in its testing area. For extra surety, forbid the test items. This will test whether Refuse stockpiles are themselves to blame for disappearing/degrading items.
2) Place two stockpiles in a checkerboard pattern, with stockpile A (checkerboard "black" squares) being a normally non-degrading item or selection (again, furniture or weapons are good options) and stockpile B being refuse or rot-able materials (food, corpses, body parts, etc.). Vermin will appear on and around the refuse, but spend roughly equal amounts of time on the furniture/whatnot. This will test whether vermin are responsible for disappearing/degrading items.
From my extensive experience in Fort mode, though, I can say with a great deal of certainty that refuse stockpiles definitely do cause degradation of items, and vermin definitely do not (for "durable" items like finished goods, furniture, weapons and armor, etc.).