Seem to recall there was a Manchester Picc-Stockport-Guide Bridge staff train back in the 70s/80s that ran right through the night,every night,usually formed of a 2 car 1st gen DMU.
Yes, there were non-advertised staff DMUs running Piccadilly - Longsight Staff Halt - Stockport - Guide Bridge and vice versa every hour through the night from midnight to 05.00 in both directions. The WTT indicates these trains stopped on request at Reddish South.
At the same time there was a Class 506 EMU shuttling all night between Piccadilly and Mottram Yard staff halt, stopping at Ashburys, Gorton, Guide Bridge, Newton (on request) and Godley & vice versa.
All this in the era when Selnec/GMT provided a regular 7-day-a-week All Night Bus service throughout Manchester - designed more around transporting industrial shift workers than late-night revelers. So no excuse for not getting to work!
On Merseyside there were long-standing staff trains on the Liverpool - Ormskirk line, which appeared in the WTT but not the public timetable.
These trains stopped at Kirkdale & Aintree, with request stops at the other Ormskirk line stations.
Through the 1970s, the times were 00.20(MX) 00.35(MO) Liverpool Exchange (later Liverpool Central) to Ormskirk and 04.33(SuX) from Ormskirk to Liverpool.
I wonder what happened if you turned up with valid ticket in hand to travel on these trains? Who would be interested in stopping you boarding?
Another example (targeted at day-trippers rather than railway staff) was a non-advertised DMU from Southport to Wigan which ran right through the 1970s.
This left Southport typically around 17.48 & 18.03 on Summer Saturdays, running non-stop to Wigan Wallgate. Presumably intended as a relief train for the regular (Mon-Sat) Southport - Manchester Victoria train running about 10 minutes later.
I know summer Saturday relief trains from the seaside were common back then, but this one wasn't ad-hoc or only for a particularly busy weekend, it ran every Saturday from May to September year after year. The train always appeared in the Mandatory WTT, but not in Public Timetables. Presumably when passengers with return half of a ticket for Wigan turned up at the barrier, the collector directed them to the earlier Wigan train, so why not just put it in the timetable?
No doubt other seaside resorts around the country had similar scheduled "ghost" trains back in the day - although I haven't found any examples for that other prime candidate, Blackpool.