- Necromancers often write a lot of books, and some of those are about the secret of life and death, so that book could definitely be one of those. The name should give an indication (in one fortress the human caravan regularly brought books with the secret of life and death, and all of those books were copies of books written by a necro. Presumably, the humans had conquered the necro tower and seized the books as plunder). The slab is the original given to the necro, but the knowledge can be transferred into books.
- The artifact weapon was probably stolen by one of the dorfs and given to the villain contact who's now carrying it. If the theft hasn't been reported yet and no other crime has been either, you can do absolutely nothing except killing the villain. If you have an injustice system in place and have at least one unresolved crime reported you can use the injustice system to interrogate and sentence the villain. According to some reports you can get the artifact back if you sentence the villain directly, but if you interrogate the villain first he won't give it up, so you have to kill him to get it back (it might be possible to use sentence the villain and use DFHack to dump the artifact to get it from the villain, but there's no vanilla way to get it back).
- There is no way to protect your artifacts that does not involve locking them away. Furniture can be placed, and won't be stolen, and artifact military equipment assigned and equipped to militia is probably safe (if the dorf corrupted to steal it is the wearer that might not work). Nothing else that can be stolen can't be protected unless locked away. Convicting dorfs of crimes has no deterring effect whatsoever (unless beatings are lethal, of course), and killing villains and their agents doesn't either, as there are hundreds upon hundreds of them (I've teleported them into the magma sea for about 50 years in my 0.47.04 fortress, and they're still coming, even though I'm running out of regular visitors since they've died off due to old age and sieges [as well as lethal evil weather]). Dorfs also have very little defense against corruption, and villains just try again if corruption attempts fail, as there are no consequences for failures.
As you can see, I find the current Villains functionality to be completely unbalanced.
- Teeth probably decay, but it takes a very long time. Bags get worn one X level in about 20 years, while wood is said to take a few hundred, and teeth are probably stronger than that still. A refuse stockpile ought to speed the decay of teeth as well, but it likely takes too long to matter if it does.
If you remove teeth from the refuse stockpile the dorfs will still pick up teeth from sapients and haul them to the corpse stockpile, which is probably what you want. One downside to not have any stockpile place for teeth is that you probably won't have any ivory for the craftdwarf workshop, which is probably not much of an issue. Another is that you'll have clutter that may look unsightly, which probably isn't much of an issue either, and I believe the 'h'ide functionality is there to not make it unsightly either (but you'd have to hide each tooth individually, unless you write a DFHack script for it).