See, I don't think I've ever boiled or even washed off a piece of corkbark in my life. I just throw it in the tank. I never really thought about doing it to be honest with you, but now that you brought it up, it does sound like it would probably be a good idea....
Yeah, when you really think about it it makes sense to boil it, just as you would a peice of wood from outside. I don't really think it's disinfected or anything before it's shipped off to the pet stores. And even if there's not any parasites inside it before it gets to the store, just think about the kinds of things that could get inside the bark once it does get there. My main concern would be mites.
I'm a fan of baking. The con is that it wouldn't remove any of the dirt that was on the bark or soaked in. The pro is that the internal temperature of the piece would get much higher. Water boils at 100 degrees Celcius plus/minus some for atmospheric pressure etc. Once you've reached boiling, you have to throw a lot more energy into the water to raise the temperature further. Baking, on the other hand, simply keeps raising the temperature of the wood.
EDIT: I don't think I phrased that thing about boiling quite right. The point is that the water won't get above 100C, you can only superheat the steam at that point.