I can get reasonable and suspicion, but the A baffles me. In this context, could someone please explain?
The rights violation occurred when the officer took possession of the pistol and ran the numbers without RAS.
I'm not so sure it was a rights violation (but then I'm far from a legal scholar). Officers have a duty to "secure" the situation, and a gun (even holstered) in the driver's lap is far from a cop's view of secure. Many times we hear of police taking guns for the duration of the stop, and returning them afterwards. Returning the ammo separately could be either the cop's personal, or department policy, to avoid any possible liability of "handing over a loaded gun".
And I don't know that running the number of the gun is a violation of your rights, either. Running your license plate, VIN number, or driver's license number is commonly done, with out asking for your permission.
I realize that the police behavior is upsetting, because we haven't done anything wrong, and shouldn't "be treated like criminals". But the police have no way of knowing that. They don't know who you are, or anything about you (or in this case, your son). Considering the situation, it seems to me like they showed considerable restraint. Had your wife and son met one of the officers who "prone them out" at the slightest suspicion (a small minority to be sure, but one that does exist), things would have been a lot less pleasant.
It is entirely possible that rights were violated during the stop, a good laywer would be the one to ask, and I'm not one. But based on your description of the situation, and actions, I don't see a strong case against the officers.