Firearms and their tactical employment are not a part of the official Bujinkan curriculum in the same way as, say, use of the sword. On the other hand, I've been told that Takamatsu sensei had no compunction about usng them when he was in China.
And I've heard Hatsumi sensei comment a number of times that a true martial art doesn't need to fundamentally change just because technology changes: It simply incorporates the new into the existing knowledge base in a congruent way which will allow the practitioner to make the best use of it.
It's not at all uncommon to see firearms use incorporated in a very natural way with taijutsu in training in Japan, and I often do so with my own students -- particularly when it comes to things like weapon disarming and weapon retention with both long guns and handguns. The same general methods applied to these skills with other weapons work just fine with firearms; the main difference is that instead of thinking about where you and others may be in relation to edges and points you need instead to be aware of things like the line of fire, muzzle blast effects, etc.
My first training in Japan was on a military mission after I'd been training here for 3 years, my battalion commander having given me some time off to run down to Noda from Camp Sendai. The instructor I was working with had me doing interesting things with a (non-firing replica) 12-gauge shotgun, Uzi subgun, and Browning pistol. That was in January of '87.
