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In my experience this can and does happen. Years (4-5?) ago a friend and myself were driving to the range, and were pulled over by a DPS officer for some unbeknownst reason. We, of course, had guns in the car (wouldn't be really possible to shoot without them!), and as soon as the officer found out, he immediately made his intent to inspect them known. Friend was removed from the vicinity of the vehicle, and the officer opened the rear hatch where we had the guns stored, and I politely asked him if I could join him and was told to stay seated in the vehicle with the doors closed. He ran the numbers on the guns we had (a few pistols and rifles - the most fancy thing in there was my Saiga 12) and I was questioned about them. Specifically the S12: officer wanted to know what "caliber it was", which was hilarious because he asked "What is this Saiga 12 gauge?" leading into the question. Asked me where I got it, and how long I had it, etc. It was pretty clear that he was fishing to see if I knew anything about the firearm to determine if it was mine or not.

Friend was back at the patrol car (just standing outside it, not cuffed or anything) and confirmed that he heard the officer call the S/N's in. They all came back clean, of course.

The kicker? The officer didn't at all care about my carry gun, NOR seeing my ID or CHL when I informed him that I was carrying. He didn't even bat an eye at or bother to look at/take my ID's when I tried to hand them to him. Pretty interesting that you would want to search someones firearms without even determining whether or not they are who they say they are, or apparently caring about the firearm said person is carrying. Ultimately we were sent on our way about an hour or so later. No citations were given, and the only thing the officer said when we asked why were pulled over was that he saw a break light was not functioning. Funnier yet? We didn't break until after he lit us up. We weren't even close to speeding or driving in a manner that could be deemed dubious or unsafe. It was a pretty shady stop all in all. I can tell you that I felt pretty sick to my stomach about the whole thing after it happened - we both felt violated because were were stopped and our firearms inspected for no reason that was explained to us other than "It's department policy" (as per the officer when I asked him). My gut tells me we were stopped because of the area we were in, direction of travel, (between Presidio and Marfa) and because of appearances (my friend's Explorer looked like it had seen better days) - IE: thinking we were from Mexico and running something illegal. Just spit balling here, though.

YMMV - Just my own experience.

TL;DR: DPS officer incorrectly profiled us, determined we were innocuous citizens, ran our numbers anyway and then sent us on our merry way.