In most cases, these secrets feel pretty natural they don't stand out or call attention to themselves like in other games that want you to realize 'hey, this is a secret area.' If you're exploring a dilapidated ruin and see a crack in the wall, you might think nothing of it, but if you peer closer, you might just realize you can stick your arm through and grab a couple extra water arrows. It's here where the level design impresses most, because there are a ton of hidden nuances to discover, from secret rooms that can only be accessed if you notice that a section of a wall looks slightly different, or if you do something completely unexpected like crawling inside of a fireplace.
Completing each of the 'steal as much stuff as possible' objectives requires you to explore every inch of the maps, particularly on higher difficulties where you're expected to steal a higher value of stuff.