It's the combination of small things that add up to make it feel creepy specifically. After looking back at the Shadow Temple in Ocarina of Time, there's several major elements that stick out to me that work together for the sense of disempowerment and fear.

First and foremost is the music. It's got this creepy chant going on in the background the entire time with low and high voices that sound like they are at odds with each other. The harpsichord part makes heavy use of half-steps, which sound naturally creepy. There's also a bunch of noises mixed in there which don't feel like part of the music. This can put the player on edge, because it can be difficult to parse the difference between noises generated by actual threats and ambient noises from the music.

Second, the gameplay itself feels unsettling because a huge percentage of it depends on the use of the Lens of Truth. The player's normal senses can't be trusted - the walls aren't always walls, the floor isn't always floor, and there are invisible threats like spikes. The use of the Lens of Truth also helps - it allows the player to fighting back against the invisible threats, but it also limits what the player can see (no peripheral vision), which reminds them that they aren't at full ability. Even the dungeon item - the hover boots require a leap of faith because Link can't control himself as well while using them (more on this theme of Link losing control of himself later). These gameplay elements add to the player hesitation and that sense of feeling unsure tickles the "creepy" sense.

Third, the art style is obviously creepy. The Shadow Temple lore says it is where the Sheikah tortured and put away their prisoners and dissidents. There are skulls, scythe blades, robed reapers, and other various death imagery everywhere. There are torture devices, spikes, and guillotines. There are rooms where the textures look like you're standing on the same kind of mass piled skulls like out of an enormous mass grave. There's even a creepy boat ride clearly meant to evoke the Charon/Underworld connection to Greek mythology.

Fourth, many of the enemies in the dungeon are disempowering - they take control away from the player which adds to the feeling of helplessness. The Gibdos (mummies) and ReDeads (zombies) can paralyze Link in place while they slowly move closer to hurt him. The Wallmasters (grabby hands) can drop from offscreen and grab Link and put him back at the start of the dungeon while the player has to watch while it all happens. Dead Hand, the miniboss, is a strong combination of both the creepy art (zombie-like appearance with bloodstains) and disempowering moveset (hidden via shadow and the bloody hands in the room will grab Link and hold him in place). The final boss, Bongo Bongo, also has giant hands that can grab and hold Link in place and hurt him while the player can only watch, and whose main body is also invisible without the Lens of Truth.

Each of these game elements individually usually isn't enough to make players feel a particular way. However, when taken in aggregate all of these different parts work together to form a cohesive experience. The death-themed architecture, the creepy music, the gameplay elements that require players not to trust their senses and to go beyond their comfort zone, and the enemies that disempower the player and force them to watch as Link is unable to act all form to make a very uneasy and creepy experience as designed. I'm sure there are other elements I missed in this analysis, but I'm also sure that any you spot will also fit nicely into these themes. Feel free to add any others you see in the comments!

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