The unregistered handgun is likely a misdemeanor at the worst. Unfortunately, if you got it from your father's estate within the past couple of decades, you still needed to register it and that would have required you to work with a dealer as well as show your right to own the weapon. I had to jump through similar hoops more than a dozen years ago when my father passed away. Though, I seriously doubt the police will care all that much to charge you with the handgun - especially since you may not seek its return.
As others have mentioned, seeking return of the firearms or even the safe may be a bit premature and should not be done with consulting an attorney. The return of the safe and the firearms will likely be treated as two separate issues. The firearms would require DOJ clearance before the return of the guns (and the .25 caliber handgun probably would not be cleared). The safe, by itself, should be a non-issue since an empty safe is not subject to being held under the law. Unless the safe is evidence of some crime it should be able to be released though it may have been damaged if they opened it to get to the guns (and they almost certainly did).
As has been mentioned, the state has time to file charges against you. Three years or more depending on the charges. And, unless the firearms are part of the allegations (i.e. you threatened to shoot her or are accused of brandishing them), then they should be released to you upon DOJ clearance provided there are no restraining orders in place against you.