Some officers are just afraid of guns, it would seem (I've known a couple like that). Personally, I appreciate it when people tell me that they are armed on traffic stops, just so there isn't any kind of misunderstanding if the gun is spotted by me in a "concerning" position during the stop. Notifying law enforcement of a gun isn't required in my state, but I've still always done it in the rare instances when I've been stopped off-duty, and my family members who carry have been advised to do the same.
My usual response to someone saying that they have a gun on them is to say something to the effect of: "okay, thanks for letting me know... just don't play with yours and I won't play with mine... hang on for just a minute and I'll be right back with you".
In most states the law allows for a police officer to temporarily disarm someone during a stop, as it sounds like this trooper did. Personally, I've never felt the need to do so when dealing with any person who has actually informed me that they had a gun. But, as you may have figured out by now, I'm not exactly an anti-gun guy.
Not all stops with guns go well, especially since I work in an area with a lot of crime/gangs. I had one recent stop where I pulled a car over that was occupied by an individual who was dressed in local gang colors (and the car had a records hit for a contact regarding gang activity). This guy's driver's side window was illegally mirror tinted so that you couldn't see inside, and the guy was acting feisty from the moment I walked up. As I approached him he put his window up most of the way at the last second, and initially refused my request to lower the window again (I was already concerned that he was trying to either gain control of a weapon or hide contraband). Anyway, as the window came back down I saw that the driver's hand was resting on top of a handgun that was pressed in between the seats. I ordered him to "show me your hands", and he started to turn into the car more, where I couldn't see if he was drawing the gun or not. At this point the guy found himself looking down the barrel of my gun, and he started saying "Hey man, it isn't loaded or anything". After explaining to him that my gun was in fact loaded, he finally complied with my orders. Turned out that he was only carrying a very realistic-looking pellet gun (certainly realistic enough to have got him shot if he had grabbed it), and had actually just used it to menace a rival gang member.
The point in all of this? Criminals aren't straight up and honest about the fact that they carry guns, and guns that are spotted in a condition like this can definitely get your blood pressure up when you're the officer standing at the driver's window. This guy gave me every reason to think that he was going to go for this "gun", and took the incident to a level it didn't need to go to ('cause he obviously wasn't planning to fight me with a pellet gun). Now, admittedly, this guy gave me a bunch of other clues that he was a bad dude, so the presence of a "gun" alone wasn't the only reason he got to take a look down mine. But, I still think there's usually some value in letting an officer know that you're carrying, just to avoid any tense misunderstandings.
In fairness, I've had cases where the good guys were carrying and didn't tell me, and I'll usually just let them know: "I see you have a gun there, please don't handle it during the stop. Okay?" I even had an absent minded lady reach into her glove box one day (forgetting her gun was there), and watched her nearly wet herself when the thing flopped out into her hand during the traffic stop. She was perhaps more surprised than I was, and quickly made it quite evident that she wasn't trying to grab a gun, so it wasn't anything that came off as threatening to me... but, again, I'm very comfortable with guns, and that could have been a tense situation for someone dealing with a less gun-accustomed officer. So, again, I think there is some value in voluntarily notifying an officer when there is a gun within your reach in a vehicle (I never notify about guns in the trunk, unless asked).
But, your milage may vary.