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Specializations give you a +2 dice pool when you are performing actions related to the specialization. So, if you are firing your pistol in "GunKata" form, you should get the +2. My guess is that HeroLab doesn't have that factored in automatically because they can't guarantee that every use of the gun is considered "GunKata."
They might have it factored into Unarmed Combat for Karate because they may have made the jump that someone specialized in Karate is going to make karate-style attacks with their Unarmed Combat Attacks.
Personally, the way I read the specializations description in the martial arts section is that the specialization (+2) applies only when you perform techniques associated with the martial art style. That would be my strict RAW interpretation.
That means that a GunKata specialization only applies when you are trying to fire your weapon for Tricking, Stagger, or while engaged in close-quarter combat. Applying that to Karate, however, means that it applies to "Kick" which is just a modification to (you guessed it) Unarmed Combat Attacks.
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