<------Former TSA agent as of less than a year ago. I think I have a bit of knowledge on the subject.
First of all, let's discuss the firearm declaration. In most airports, there is essentially no communication between the Airlines check-in agents and the TSA about individual bags. You had a locked bag, which is totally fine. The declaration was likely inside. At this point, there was no way for the agent that opened your bag to know there was a firearm inside. Should there be better communication? Yep, I argued that point for years and it fell on deaf ears. Typically, the Airlines hate the TSA and will do everything to blame them for problems and make their jobs difficult. In turn, TSA will do only the bare minimum as far as working with the airline. Hence, not much communication. So unfortunately, there is basically no way for the TSA agent to know there was a firearm in your bag.
Now, about cutting the lock. Using the "master key" (TSA's special name for the bolt cutters) is supposed to be a last resort. They are supposed to hold onto the bag and have the passenger paged. The airline should have let you know to wait, or where to wait, or whatever. Only after a reasonable amount of time has elapsed are "destructive" methods of entering a bag supposed to be allowed. Unfortunately, TSA won't have a record of your exact bag, and if you were to complain, they would just say that procedure was followed.
Now, it is completely against the rules to cut the locks on a gun case. I imagine your declaration form was near your gun case in your bag. They would have been required to page you and have you open the gun case, in this case (or "lend" the keys or give the combo). If you couldn't be paged, the bag would not have been allowed on the plane, so there would be great incentive to get you paged. The thing is, the locks on your suitcase wouldn't be considered the same way as the ones on your gun case. Your suitcase locks would have been fair game for the bolt cutters, whereas the ones on your gun case would not have.
Now, in my 9.5 years with the TSA, I think I cut maybe 10 locks in that time. It was incredibly rare. I went to great lengths not to destroy people's property. Unfortunately, there are people who are trigger happy about getting a bag opened, and will bend the rules a bit to save them from having to *gasp* talk to someone! Whoever cut your locks was completely in the wrong. That should not have happened, especially since you were actually waiting.
The only recommendation I can make to prevent this is to use TSA locks. I am well aware of the issues regarding them, so it's your choice to use the TSA locks, or risk another incident like the one you went through. Unfortunately, there's likely almost no recourse for what happened to you. I wish it were different, and that is one of the many reasons why I don't work there anymore. So much stupid, so little common sense, and anyone with a GED can work there...
EDIT: Just read this.
While there is no label advertising to the general public that a firearm is inside, from a standpoint of anyone hooked-up to the baggage handling computers, the suitcase is in fact clearly labeled. To the TSA and the airline, it is indeed clearly indicated that a firearm is inside.
You assume a couple things.
1) That TSA scans the tags. I've never done it, and I've never heard of it happening. They might be scanned so they can be routed to wherever they need to go in the airport, but it's very likely TSA isn't hooked into that system. All the information the TSA needs is physically printed on the tag (and all TSA needs to know is selectee status). Remember what I said about the airline hating the TSA? They wouldn't give TSA access to this system unless they were required to by law.
2) You assume that even if they are hooked into the system that they would actually use it. I'm not excusing this kind of behavior...it's just the kind of thing you see fairly often.
