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I'm not sure I understand what the concern is about running a check on the weapons. The officer is allowed to temporarily disarm you for the duration of the stop. The serial numbers are in plain sight on the weapon, unless you turn over the weapon in it's holster. Either way, the material condition of the weapon is not affected.
As I recall, the stop was initiated because of an alleged traffic offense. The car is not the perpetrator of the offense, but among the first things the officer will do is run a check on the license plate to see if the car is stolen or the owner wanted for any offense. How is one okay but not the other?
Before I get flamed here let it be known, I really really hate for someone else to handle my guns for any reason whatsoever! Doesn't matter if it's a LEO, or my father. If I have to allow it though, I would rather the officer was thorough and professional. From what I could read, it sounds like he was a decent sort. I have had worse experiences......