In summer,carp actually attack a feeder to get at the bait inside it,so they cant be that put off by foreign objects thrown in amongst them,i dont believe the feeder is completely invisible to them.....
Chefster you need to look at the broader picture. Most waters you'd opt to use a method feeder on will presumably have a high stocking density, which by their very nature removes much of the innate wariness fish display.
Taught line is a prime example; put a tight line in front of heavily pressured specimen carp that lives in a sparsely stocked water, chances are if it sees the line it'll steer away from it.
If it swims into the line, it usually spooks the hell out of it, with the fish fleeing at speed.
Whereas on heavily stocked waters they don't tend to behave in such a way. Usually they are seemingly oblivious to fishing line.
Big carp, even on low stock waters can be readily taken on a method feeder but if caught a few times in a short space of time, then they often back away from method feeders.