Well, the different sub/special weapons are definitely one possibility, but do keep in mind that different brands of the same weapon might end up functioning in different ways. For instance, what if the Tentatek Splattershot has slighter higher range but slightly higher ink consumption than the normal one? These are the kinds of small modifications I can see from branded weapons. You see much the same thing from a game like Borderlands 2--each manufacturer has certain "specialties", so one brand of guns has higher damage than average, one has higher magazine sizes, one has higher accuracy...
I imagine those two things will work in concert. Yes, you'll get a different secondary weapon and special... but you might also be affecting the base stats of the weapon by using a specific brand, making it a potential trade off.