Clockwork's greatest strength is also his greatest weakness. Namely, that he's a rigger. Riggers rely primarily on their drones to fight. Hackers, on the other hand, excel at taking over and turning a system against the user. Take, for example, the game that Netcat and Slamm-O! played in the SR4A book. Sure, a surveillance drone won't have the same kind of security as Clockwork's combat drones, but if they subvert a couple of his drones, and make them target the drones he still has control over, that negates Clockwork's biggest strength, and also serves as a distraction for someone else to get in close to his meat. That's just one scenario, obviously, but the point is that Clockwork is one person, and Netcat has allies, in the Matrix and out.