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.
Best Answer
If you're careful, you can sneak hacking (and boarding drones!) past any number of defense drones with a combination of timing and power management.
Your Drones of all types only move when they are powered. But what is less well known is that they can only be destroyed when they are powered. If a Defense drone's attack passes over an inactive hacking drone, nothing happens.
This means you can develop a subversive sort of hacking strategy through judicious use of the pause button: Launch your drone, then, when you see/hear the defense drone fire, pause the game, and unpower your hacking system. As soon as the defense drone's projectile passes over your hacking drone, pause again, restore power, and the hacking drone will start approaching again. To get all the way to the enemy ship might take one or two pause-depower-dodge cycles, but once you're attached to the ship, you're golden.