In GURPS Traveller most vehicles have access to a program called Routine Vehicle Operations or Autonomous Ops, which allows a computer controlled (fly by wire) craft to pilot itself, providing it has the correct sensors. The ship doesn't become Han Solo, so no acrobatics, just routine things, like take-off landing and such. It would probably be a disaster in certain situations, like in a heavily trafficked area, or where weather really comes into play, or sensors are trouble.
However I could see the ship's main computer being tied to say a captain or engineer's handcomp to engage certain programs at the push of a button; such as RVO or Anti-Hijack or Datalink.
I'd also say that someone travelling on the ship with the correct equipment might be able to exploit the access point (if it's wireless) or simply remove the terminal in a cabin (if one was offered) and jack in their own...provided the equipment they bring is correct.
As for assaulting the CPU/server of the ship, that might run into problems, especially after TL9 where it can probably lockout certain terminals it feels are for example, repeatedly trying to login to break passwords.
There's probably ways around this, especially where creative players are concerned, like getting the system to reboot itself and replacing one type of terminal with another during the reboot cycle such that when it comes back up, it thinks the device is something harmless and doesn't monitor it.
So it falls mostly to the GM.
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