Not sure how many players run hacking ops, but here's a real-world article about them hacking a 757. It doesn't go into details of exactly how, but you can Google other stories about hacks of vehicles like cars to get a better understanding of what's possible.
http://www.dailymail.co.uk/sciencetech/article-5077043/Boeing-757-controls-remotely-HACKED-runway.html
In this particular case they didn't have to jack into the system (which if a person were on a starship they'd have to). While systems are different I think you can gain an understanding of what's possible (and countermeasures) by doing this. In the case of worrying about passengers hacking a ship in-flight, you could have the ships control systems on an entirely separate network from what passengers have access too. This would be less likely on smaller tramp freighters, but it would be reasonable to have a paranoid owner re-wire a few things to do this. And you could toss in ways to make it hard to bust, like quantum encryption on the fiber optics (or whatever passes for that in the future) which makes physical interaction pretty damn impossible. An enterprising hacker might be able to create a method that would allow them to 'sniff' the transmissions, but not necessarily hijack them w/o say setting up a feedback loop and tricking the system into thinking his commands are the correct ones.
Just one idea. There are literally too many to calculate, so use your imagination refs!
http://www.dailymail.co.uk/sciencetech/article-5077043/Boeing-757-controls-remotely-HACKED-runway.html
In this particular case they didn't have to jack into the system (which if a person were on a starship they'd have to). While systems are different I think you can gain an understanding of what's possible (and countermeasures) by doing this. In the case of worrying about passengers hacking a ship in-flight, you could have the ships control systems on an entirely separate network from what passengers have access too. This would be less likely on smaller tramp freighters, but it would be reasonable to have a paranoid owner re-wire a few things to do this. And you could toss in ways to make it hard to bust, like quantum encryption on the fiber optics (or whatever passes for that in the future) which makes physical interaction pretty damn impossible. An enterprising hacker might be able to create a method that would allow them to 'sniff' the transmissions, but not necessarily hijack them w/o say setting up a feedback loop and tricking the system into thinking his commands are the correct ones.
Just one idea. There are literally too many to calculate, so use your imagination refs!