In Chapter 2 (Playing as the Thief character), in the Osohe Castle, there are two doors like this, one in the basement, and one on the upper floor (past Mr. Passion).
Upon interaction with the "door" (which is more like a stone face in the wall), I receive a message that says: The sound of blowing wind can be faintly heard coming from behind this wall.
I am playing an English-fan-patched ROM of Mother-3, so the quote might not be accurate.
If the doors are supposed to be opened later in game, or it is a puzzle, just say so, and hide the details in the spoiler tags.