[Edited]
I also have no end of problems with Virus (it's not in my Traveller campaign), but I could see something interesting with AI controlled ships with some sort of cyberwarfare systems.
Mass Effect 2 did a good job with the whole shipboard "cyberwarfare suite", which seemed to be a sort of combination of ECM and fairly specific computer intrusion systems. It made sense, since (Reapers aside) most of the foes a ship could expect to meet in that universe were from relatively well-known races with well-known ship designs. A warship might have systems specifically to help it interfere with Batarian starship systems, for instance. This would rely on the military having up to date intelligence on Batarian systems, but that's what intelligence organizations are for.
I could easily see the same thing applying in Traveller. Knowledge of Zhodani starships and computers could allow a warship to use cyberwarfare systems to interfere with the shipboard systems on a Zhodani ship, while defending against similar attacks. I could see this going to either extreme: Perhaps it's little more than a nuisance to the targeted ship, or perhaps it goes the full "Wrath of Khan" route and shuts down vital systems in the middle of a firefight. Personally I'm leaning more towards the former than the latter, but I could see a successful cyberwarfare attack applying a negative DM to the target ship's rolls.
Since my own players are Scouts, and the IISS is an intelligence organization, I could see some interesting adventures surrounding attempts to gain knowledge of some new piece of Zhodani technology in order to keep Imperial cyberwarfare systems up to date... :devil: