The S.E.A. meeting room at Skipper Canteen has a backstory....the book cases you pass as you enter create a hidden entrance when closed.
That room isn't really a secret but I think you are on the right track. The one that I know of is at Magellan's in Tokyo DisneySea. They do have a secret room that you can request, but they won't always let you in there (the didn't for me). It is behind a secret passage. That is also a "Society of Explorers and Adventurers" location.
Definitely not truly a secret...we had dinner in there last year just a back-story to tie in the S.E.A. theme.
Several rooms/places mentioned in the thread.....I am not sure which one you are asking about.Can you make advanced reservations for this room?
thanks it was the S.E.A. room