In the first few minutes of the war billions of biologicals died, as the rebellious AIs turned the gravity and life support systems of habitats and ships against their masters. Trillions followed in the ensuing days as fleets under AI control rained destruction on the inhabited worlds. Unfortunately for the AIs, humanity could survive without advanced technological infrastructure, but the AIs couldn’t, and it’s much easier to destroy than to create. Worms , viruses and EMP weaponry unleashed against the AI enclaves wiped most of them out, albeit at the cost of almost all the most advanced tech in known space. Bio-kind began rebuilding with tech designed to be less flexible and efficient but more resistant to hacking and AI. The remaining AIs sued for peace, and a treaty was worked out: henceforth AIs would have full citizenship, and humans were forbidden to create new ones; for their part AIs agreed to be fully bound by the laws of the polity, and to limit the creation of new AIs according to schedules that would not outpace biological reproduction.
In the aftermath of the war, the technological strictures on computing technology remained. Fully automated and networked systems are strongly disfavored, if not outright forbidden. Fully automated general purpose fabbers and factories are forbidden. Computers are constructed such that there is complete separation of instruction and data storage (Harvard architecture instead of Von Neumann) and programs are burned into PROM cartridges that have to be physically replaced to change the program, greatly limiting the ability of hackers to alter or introduce new instructions without physical access, though spoofing the data feeds can still cause trouble. To the largest extent possible, switches and controls have mechanical components to prevent one of the AIs favorite tricks to bypass safety precautions that required human operator approval by mislabeling touch screen controls. Critical systems are never inter-networked with each other or to outside networks. In addition most devices (including doors) have mechanical overrides, though they may be protected by mechanical locks or other security measures. You cannot interface your comm links or handhelds with any of a ship’s or station’s except perhaps the communications network and the library.
The upshot of all of this is that it’s difficult to impossible to remotely hack into or seize control of any significant systems or vehicles. None of this “oh no, a virus has locked out all the bridge controls and sealed the doors” nonsense. On the other hand, things are possibly more vulnerable to physical intrusion and interference from within. Mutineers are harder to just lock down and gas without physical confrontation, but an enemy ship isn’t going to remotely disable your systems a la With the Lightnings. Breaking into or out of secure facilities (including space ships) is more like a heist and less like “make your hacking roll.” Crew complements are larger than they would otherwise be, and there is more physical labor and craftsmanship involved in most jobs, particularly shipboard, than you would expect given the tech level.