I do remember some of those rumors. Seems like one involved that flute you find in Dragoons' Caverns; I think they said to hold it and dance around that sword-in-stone that's just outside New Sorpigal to bring in a special goblin, or something similar. It's been a while, so I don't recall too much about it now.
I would think that the only "Secret dungeons" would probably be the NWC office Easter Egg. Which, I think, was intended to be a nod to everyone who worked at NWC at the time, as if you hover your mouse over the NPCs there, it shows the name of whomever worked in that area. You can't talk with them, but it's still a nice way to recognize the behind the scenes workers.
In MM7, you can speak with the workers in the NWC Office, but no one has anything to say.