Late Mabey a hacking station can only have one hack thing at a time, and it slowly chews through different parts, disabling them with hacks?
The counter would be to:
A ) disable parts adjacent to the hack. The hack will die if there is no parts to hack, and it can’t hack disabled parts.
B ) Security station
C ) Out of range. The hack station needs to be in close range to the target ship to function (like, really close)
D ) Have the hack station destroyed
E ) Unplug replug! (I.E. turn off a hacked part and turn it on again and the hack will be gone)