I sort of disagree with... Everything that Marburg says. Sorry.
The idea of a chip in everybody's head that makes them be able to fly, send credit transfers, operate the ship's beamery, and everything else that people blame on the NN is slightly ridiculous to me. Mainly because if it can do all that, we're getting into the range of Mass Effect style biotic powers. In addition, if it the chip helps them fly to such a great degree that without it their mortal minds would be crippled with the complexity of the ships implies that you might need, maybe ten people for something the size of a dreadnought to control all the systems aboard.
Aside from that, since every electronic device can be influenced from the outside in some way, shape, or form, then (going along with your headaches) it stands to reason that you could overload and explode somebody's head by making their chip access a hundred and one different functions.
