Off of the top of my head, I can think of a few reasons why this might not work. A large spaceship would have its own communication network or networks, and I can't really think of a reason why an intergalactic-capable civilization would leave any part of that network exposed such that an external enemy ship could get access to any part of any network. Of course, friendly ships must have some way of communicating with other friendly ships, but I assume any such communication link would be extremely well defended and possibly even airgapped from the rest of the ship's systems.
There are huge incentives in space warfare to not actually pursue combat that could destroy ships. First, space vessels are going to be WILDLY expensive under any rational system. If you could defeat an enemy using cyber warfare, you could not only stay well out of range of conventional weapons, you could also capture their vessel completely intact. If you don't particularly care about human lives, you could just vent the ship and voila, you have acquired a perfectly intact, unmanned vessel of incredible value. If you do care about human lives, you could ransom all those thousands of people back to their side (for a nice chunk of change) and keep the vessel anyway. Furthermore, if neither side of the conflict inspires significant loyalty in their troops, you could just acquire the vessel wholesale, completely ready for action.
As may have been clear above, I can't really picture what sort of cyber defenses and attacks would be possible in a intergalactic-capable civilization. They would be quite unimaginable in my estimation, so far past our own current capabilities as to be unrecognizable. What I can guess is that, as soon as we invent cyberdefenses that seem unconquerable, someone else will invent an attack to conquer our system. As soon as that attack seems unstoppable, someone will invent a way to defend a system from it. This arms race will continue all the way up until the setting of your world, which will most definitely have some flavors of attack and defense. One side may have the temporary advantage, but sooner or later their will always be a new exploit.
It might be possible to create a system that is completely invulnerable, or an attack that is unstoppable, but I doubt it. I would guess we don't see cyber warfare on the silver screen because it doesn't make for particularly compelling television. In real life, I believe militaries would use every tool available to them, including cyber warfare.