They ARE invisible. In fact, you should make it a habit to check anything and everything. Often things are hidden in drawers, cupboards, bookshelves, .....
Plus, in the MM series there are lots of secret rooms to find, and in some of them there's great stuff. Often secret rooms are in fairly obvious spots, like niches or where there's a crack in a wall or something like that. But The Trickster always hides some that are really tough to find because nothing indicates that they are there. When you find a SR you should always note down its number and location. If you miss one you can then more easily narrow down in which area it's most likely to be.
In dungeons always try to jump down cliffs because sometimes you'll fall into a SR. However, in order to access some of the SRs you need a special piece of equipment, the
Air Sandals that make you jump higher