I work for a brewery producing ~50hl of beer, and we use pellets (for a variety of reasons). But, yes we use pellets. Even the three local smaller breweries (with brew houses of 3.5hl to 12hl) use pellet.
I have been on many brewery tours and usually ask this question. The response is overwhelmingly pellets. It seems to be only the bigger breweries I've been to that use whole cones. Victory is the only one I can think of off the top of my head, but I think Harpoon may have ask well...
My friends who work as brewers all use pellet hops. In one case at least, it was because their system couldn't handle whole (leaf) cone hops. It worked out for me, because when a salesman gave them pounds of hops to try, and they were whole hops- he gave them to me!
Dogfish Head and Harpoon both use pellet hops...seen them on tour and asked...Cape Cod Brewery in MA uses both whole cone and pellets from what I've seen