How can you hack a system without a hard line? If the drone is autonomous, it's not receiving target data from it's mothership. There's no link to disrupt. If the drone's target is preprogrammed prior to launch, and heads out to do it's thing. And has no sort of data recieving method other than its sensors, how can it be interfered with, aside from direct attacks??
People probably point to the BSG episode, Separate or whatever it was called, season 2 ep 1 where the BSG loses the fleet and gets hacked by the Cylons while they're doing their calculations. but I've heard more than a few people say that's a pile of BS.