You'd have to hook it up to their network, which means you'd have to get into their ship. Maybe you could find their frequency and flood their transmitter with useless messages but good luck with that.
if you get physical access to their ship, you could modify the values of any device they have on the network with a chip. assuming they don't change the default external variable names. essentially you could have a chip for each ship type that holds a payload allowing you to control whatever devices you want (again assuming they haven't modified their defaults)
Maybe to hack someones system, you would need to swap out chips with corrupt ones, maybe there needs to be certain firewall chips hidden somewhere on your ship which lock out all the other ones to prevent swapping?
Essentially you would only need to make turrets go different angles or thrusters making you spin out and doors opening and closing and just generally cause Chaos onboard the ship, sabotage comes in many different forms, lots of disrupting elements at a time or one more subtle one that takes longer to find
you can probably just rename the thrusters and need a reviver and a few chips and you can fly anothers ship remotly.
just depends on how good you can sneak into their ship and how much time you have untill they will notice it, since they can allways just destroy the logic cables that go to their thrusters.
I'd say, it may be possible to have code copied/have one of those drives with the code loaded, sneak onto their ship, and load it into a drive rack (If they have one) From there you'd have to find a way to activate it, or perhaps if your code would scan on input from some sort of message from the ship to set into action.
If you can change the name of their systems and they have a radio transmitter/receiver, you can send messages to their ship that could trigger commands, such as shooting the mounted guns into their own ship.