Take the first island as an example.
Look at the top-left and the top-right snakes. Their eyes emit red light.
This only happens when the room has secrets has not been exposed.
The snakes can reveal secrets such as hidden stairs, hidden passages, and musical notes (I see many people ask where the notes are), and their eyes will close after all secrets in the room have been found. (Like the example below, the hidden stair found and no red eyes)
About the music notes, there will be a nearly transparent music note emblem on that block before you pick it. So keep your eyes peeled if you see the eyes of snakes become red. The notes are especially hard to find out when they're on the ice blocks.
Good luck.

However there is at least (or only?) one exception, a hidden passage that is not hinted by the snakes.
(But it is a black gem so not related to any achievement or ending requirements? So feel free to search it on your own.)

It is on the island you can only reach it by the huge bird ride. (Bottom-left of the world)

The exact passage is shown below. I also highlight the 'hidden passage/staircase' mark by the red rectangle. If you see the mark in other places, try to push everywhere then!

Screenshot here, the secret passage is the shallow water at the bottom