Yes, by default VIC has been working hard to get on the Hegemony's good side, and if someone (like, say, the player :V) doesn't work hard to put a wedge between the two, they will often end up allied.
In my own experience, though, VIC doesn't dominate that hard; even in the new patch, they kind of seem to struggle as an NPC faction. They especially have trouble with station sieges, as a lot of their ships and their AI isn't well set up for siege warfare. Taking on anything bigger than an orbital station can be a challenge for NPC VIC. It helps keep them in check, but trying to help out your commission-mates can get a bit frustrating when Apolloyons suicide against a battlestation's guns. :V
I do have to agree that the lack of medium/large missiles feels... odd? I know VIC also outright uses "base" weapons like Tach lances, but it does feel odd that they have ships with the larger missile slots and no in-house solution for arming them at all.