I toured a US missile sub a few years back with a group from Microsoft. We went into the launch control room and saw a Windows PC running NT 3.51 (or maybe 4) on the control desk. Our reaction was, let's just say, extreme surprise.
The two guys in the room (I'm guessing that room is always manned, even during a refit) immediately understood our concern. "No no," they said, "that's not the missile computer. That's the missile computer." They pointed behind us at a giant grey metal cabinet. I imagine the technology was from around 1980, but from the look of it I wouldn't have been surprised to find vacuum tubes inside.
We were all quite relieved to find that nuclear missiles are controlled by an old computer that presumably doesn't receive security bug patches on a weekly basis.