Both MK II and the mother ship's defense drones seemingly create an impenetrable defense against hacking.
In particular, the second stage mothership has a single defense drone. Even when part of a large volley of other projectiles, the defense drone unerringly singled out the hacking drone to shoot down. I tried sending it out slightly after a large volley as well; similarly no luck.
Is there a trick to get around this defense, in conjunction with regular/ion weapons? Perhaps some timing trick? I've often found that the computer's attack drones somehow slip by my own defense, though perhaps they're simply slower than the mother ship's.