In the real world, it is possible to design a computer system that is foolproof against hackers. For large systems, it may be overly complex. However, for their stupid wireless communications,
- If it's an analog signal, they don't do any processing on it, which means there's no chance it could hack the system.
- If it's some sort of encrypted digital signal, the small amount of code that decrypts it could be checked for ridiculously improbable security holes, and then again it wouldn't be a problem.
Finally, just have a big computer system dedicated to FTL, as it needs the processing power. Nothing else on the ship needs anywhere near as much processing power, so just have the Cray supercomputer be isolated from the rest, and voila, problem solved.
Really, I program for a living, so I can definitively say the network thing, while being cool, is entirely unrealistic and retarded.