When a hacking drone has latched on to my ship, is there any way of removing it? What about disabling it?
The only way you can disable them is by damaging the control room on the enemy ship, I believe. I'm not entirely sure but I think the drone that can shoot down incoming projectiles may be able to destroy it before it latches on although this will require good timing. Also an ion shot to the hacking control room will temporarily disable the hacking bot.
There is a way to (temporarily) disable hacking drones without destroying their ship or wrecking their hacking room.
An odd defensive option you have in the event of hacking drones is hacking their hacking room. When activated, this will prevent (or interrupt) their hacking process. I personally don't do this very often as I find hacking shields/weapons to be more effective, but in rare circumstances it could be handy, such as when they've hacked an area of your ship that blocks movement to critical sections (bottleneck.)