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There are several questions hidden in this situation that may provide very different answers. The first side is the legal side, some of which may be debatable. Let's start with the running of the numbers. I have always been taught that this is a search, which may or may not be correct or make a difference in your logic. I am going to continue to assume that this is a search. Then comes the question of if this is a legal search. As a general rule, may seize anything in plain view where he is legal to be. If he legally comes into possession of the firearm, running the numbers would be legal (assuming they are visible without field-stripping the pistol). So, you have no way to object legally to the running of the numbers once the officer has the gun.

Which gets us to the question of seizing the gun. While the officer asked int his case, I will point out that he has the legal authority to seize event he cased guns. The law (GC 411.207) says the officer may disarm the CHL. It does not say just the one gun or any gun on his person. Leaving a person in possession of even cased guns means he has not been disarmed. So, the officer can legally take the cased guns. This, of course, presumes that there is no legal question of officer safety, which is a requirement for taking the guns.

But that brings you back to the search of the seized gun to get the number. If the gun was cased, I don't think the plain view rule would apply to the serial number. There are other legal ways to get into it, but they are sort of outside the scope of this type of stop. In the instant case, since the OP consented, they are also irrelevant, as is even the plain view rule.

That gets to the question of whether or not you should consent. This is a personal decision. The things to consider are your desire to stand on your rights, your desire to privacy, your willingness to cooperate with the police, your trust of the police and government, your trust of your knowledge of what could possibly be found (did you buy the gun used?), and your desire to continue on your way. The old saying "go along to get along" may hold true. Your are much more likely to get a ticket if you do not cooperate in the officer's desires. That may not be right but is fact.

Which gets us all to the last question. If the officer does not get consent, what can he do? Legally, he must develop probable cause or let you go. In reality, some officers will search anyway, even though it is illegal. They know that absent some real harm (and the courts generally will not hold the delay or search as enough harm), you won't get anything from a lawsuit and they may not get any real punishment from the department if you do complain.