Short and sweet. Gun safes have a lot of different functions. They keep little fingers off of things they shouldn't be touching. They do the obvious of protecting your stuff from criminals and fire. Oh, and one last thing. It can be one last layer of 4th Amendment protection for you at your most vulnerable moment.
Soooo... It's a justified self-defense shooting. I don't know why in the world law enforcement would take it upon themselves to confiscate firearms and ammunition that were not involved in a shooting. Maybe there were other circumstances (ie felon in possession), but I would think you'd be reading about the arrest of the homeowner as well. I'm not even a fan that they would confiscate the firearm used in a self-defense shooting in a home. This is a perfect example of why Clint Smith and Massad Ayoob say you should have a scripted response for after an incident and then say you will cooperate fully after you speak to your attorney. And no, you cannot take anything from my home without a warrant or without speaking to my attorney. No, I'm not opening that safe without a warrant. Now the homeowner is potentially defenseless against the retribution from thug friends and/or family. Good police work there, Barney.
Also, based on the comments of the Commonwealth's Attorney, Virginia is in dire need of a well-written Castle Doctrine.