The hidden places of Hyrule are those places that the average traveler, sticking to the roads and following the signposts from one point of civilization to the next, would never find. They may be merely hidden from prying eyes, or their entrances might be sealed, accessible only to those who use a specific item, ritual, or arcane passphrase. They often hold some kind of treasure, perhaps with a story that tells why the hidden place is so secret.
A hidden place is not the same as a full-fledged dungeon, secret village, or other location of true adventure, mostly due to its size. Instead of being large enough to have eight or more encounters, a hidden place is generally only one or two encounters long, with the biggest hidden places structured more like a delve with three or four encounters. They do not replace or create their own adventures (at least, not on their own, though they can be hooks for other, bigger adventures elsewhere). Instead, they serve as distractions, interesting places to visit and things to do, while 'on the way' to the next important destination.
This doesn't mean that a dungeon, temple, or other place of real adventure cannot be hidden away - merely that they should be hidden away better. In fact, hidden places can sometimes be found within such areas of true adventure!
Since hidden places are meant to be 'between' the more important locations of the world, they typically will be found while the party is traveling from one location to another. This can be handled a number of ways.
Skill Checks: As the players make their way between place A and place B, have them make a skill check to find hidden places. Perception works well for all cases, but you may also want to include Arcana, Dungeoneering, Nature, or Streetwise. In fact, depending on the exact nature of the hidden place and its surrounding environment, potentially any skill could be used to find it - even skills like Insight or Heal!
Passive Skills: Much like the above, except you do not call for a roll. Typically only used for passive Perception, this can be useful if the party is in a hurry, and not dallying around to look for interesting nooks and crannies.
As a Reward: The hidden place may be difficult, if not impossible, to find using only the party's skills. The party could receive information as to the location of a hidden place as a minor quest reward, or even secreted away in a different hidden place!
Many hidden places require, intentionally or not, the use of a specific spell, item, or technique to gain entrance. The party may also require specific knowledge about the task in order to be successful, especially when the hidden place is revealed to them as a minor quest reward. Usually, the obstacle that prevent entry into the hidden place needs only to be passed by a single person, who can then easily flip a switch or open up an alternate route that others can use to gain entry into the hidden place. Some examples include:
A heavy block that must be put on a scale, inscribed with the runes of Tenser's Floating Disk
A large gap that can only be crossed through use of the Hookshot
A wall of impenetrable vines, undone by plucking the correct flower
Many hidden places have small puzzles or challenges that guard their treasure. Some common examples include:
A room with an ice floor, where blocks must be pushed onto pressure plates to open a gate.
A group of Elite enemies, where terrain is to their advantage.
A cave of magical darkness, with weak Lurker enemies.
Most hidden places will have a 'prize' at the end, a treasure that makes exploring it worth the effort, typically about one Treasure Parcel's worth. Some common treasure to find as the 'prize' of a hidden place:
Money (Rupees)
Valuable mundane items (a necklace of precious stones, or expensive ancient amber)
A magic item of relatively low-level
A Piece of Heart
Collectible items (Golden Bugs, Rabbits)
Useful, but non-unique, ritual components