I feel that as a passive quality, it's technically questionable, but as as Balience standpoint, I see little problem, namely that yes it is playing to obtain an advantage but then why shouldn't he? Considering he's giving up...

A better weapon (generally 2 handed weapons are better as pure combat weapons.)

Wielding 2 one handed weapons (harder difficulty, potentially more damage)

Interaction with objects. (Something a character can do with one handed and 2 handed weapons, not duel wielding.)

Two manvours to draw both weapons.

Range (short/medium, though there is one long pistol.)

Though that being said, though generally the raw is that you must wield both weapons, not merely hold it. Thus all penalties should apply. That being said, I am in the camp that prefers rules of cool, the same reason I am trying to design an design an attachment to a dueling pistol to make it a six shooter.

So do what's fun, just as said, apply whatever you give to your npc the same rules your player has.

If a player is carrying 2 weapons and choosing not to use them for 2 weapon combat there's nothing that actively prevents the passive non-offensive benefits from unused weapon B from affecting them. Outside of melee range it won't really be a factor.

1) Make them take the 2 maneuvers required to draw both weapons

2) Shoot them so the Defensive 1 is meaningless

3) Add setbacks for carrying 2 weapons/upgrade difficulty for wielding 2 weapons of different types by 1 even without using them for two weapon fighting

4) Use additional threat (for less than the 3 Advantage/Triumph listed) to make them drop the unused weapon to put both hands on the gun to steady their aim