The Scathing Bay is a crater left after Baar Dau's fall where Vivec city used to be. TES III takes place years before the catastrophe, so you can visit Vivec before it was destroyed, with Ministry of Truth (Baar Dau) still safely levitating above it.
I'm not sure about secret rooms. One of the guilds' headquarters is hidden near Vivec's sewers, maybe that's the place you found?
There are a couple of hidden doors in the towers at Tel Vos. Plus there is the Secret Library in Vivec.
Best I move this to the CH&S forum.