Well, there's two programs that run when UD starts... There's the actual ligandfit app, and there's the agent. I've managed to kill the agent (and keep ligandfit going, without showing anything), but the agent is responsible for going out and getting more work units, etc. I haven't managed to get that running without a display, ever.
Apparently there's a linux CLI version of the agent, but ligandfit doesn't work under linux. Perhaps they've made a CLI version for windows that would have better luck working in the background?