Protocol for being stopped while CCing

Howdy, folks. Just found the forums a short while ago, and figured I'd access the combined knowledge of people that have been carrying a lot longer than me.
(Already scanned through the forums, couldn't quite find what I was looking for, thus the brand new thread.)

I've been carrying since February of this year; IWB Crossbreed Supertuck, carrying an XD9 Service in black. Good holster, good gun, good times.

Anyways, story-time. After taking a friend out to dinner and then dropping her off, I was stopped by a local sheriff squad car on my way home. It appears I had let my license tag expire (never got the damned piece of mail).

I pulled off to the side of the road, yada yada, complied with his instructions. Had my driver's license and my CCW permit in my hand, with both hands on top of the wheel. He asks me if I'm currently carrying, I inform him that I was, so far so good.

Eventually, he asks me to step out of the vehicle, and I comply. Then, he asks me to unholster my pistol and hand it to him. I do so, informing him that it is condition one (round in the chamber, ready to go). He attempts to drop the magazine...and is unable to. Eventually, he needs to hand the pistol back to me twice in order to clear it; once to drop the magazine, and once more to rack the slide and get the loose round. It ends up on the hood of his car while he runs my CCW permit.

After that's done, he then proceeds to run the serial number on my pistol. This entire process takes a good long while, and another sheriff pulls up to lend a hand. In the end, he sees that everything is in order, and let's me off with a warning to get my tag renewed.

Now, my question is such. I've been told by some folks that the cop running my pistol's serial number without any probable cause is a 4th amendment breach. What's the real legal bit for this? Are police officers allowed to run a pistol's serial number even if the CCW permit checks out and there's no PC?

It's not the first time I've been stopped by the police, but it was the first time I was stopped while carrying. Since I figure that eventually I'll be stopped again for whatever reason, I see that it would be best to know what's supposed to happen and what to do.

Thanks in advance!