A few years ago I read a story set on board a military spaceship, where a character uses cartoon character names to designate operational contingency plans, fearing that their communications are being monitored.
Possibly a Babylon 5 novel? Babylon 5: Voices Security Chief Michael Garibaldi has a fondness for cartoon characters (his second favourite thing), Babylon 5 is run by the military and they are surrounded by telepaths - some of them people noted for spying on them in episodes of the TV show.
In David Gerrold's Star Wolf series, the ship is infested with "Imps" who are monitoring the ship's internal communications. In order to coordinate a shutdown and isolation of all systems, the ship's AI has generated what the crew believe to be nonsense phrases to be used as code words. Each phrase was actually the opening words of a classic story, "It was the best of times, it was the worst of times...", "Call me Ishmael.", etc. Not cartoon characters, but the exact situation otherwise.