what separates a Zelda dungeon from a typical D&D dungeon. From what I can tell:

-more focus on puzzles

-spacial reasoning based design

-more focus on the macro challenge (navigation, “solving the dungeon”) over the micro-challenges (combat, puzzles, traps)

 What do you think? How could you implement this in a d&d dungeon. What challenges would arise from translation to a pen and paper context?

Well, I don't know the answers to your questions... I just know that I'm now going to incorporate at least one Zelda dungeon, room for room, into my current D&D campaign! I'm thinking the Water Temple from OoT...

I love using the Legend of Zelda games for dungeon inspiration, and I think your points have the gist of it. 

I'd also add that Zelda dungeons are often tool focused things where there is only one way to solve the puzzle. When you get the hook-shot, boomerang, mirror shield, etc. you have to use it to solve most of the next dungeon's puzzles. I think this concept is sometimes lost in games like 5E because generally players want to use their character features and creative problem solving to figure out the puzzle -- rather than just the items the DM awards to them.

For instance, I had set up a puzzle encounter that required five levers be turned in the correct sequence; the levers were in different rooms and on different levels of the dungeon. The system was fairly easy for the PCs to coordinate, but the catch was that there were only four PCs. Who would turn the fifth lever? As the DM, I realized this problem and placed a magic item earlier in the dungeon that allowed the person attuned to it to cast the Unseen Servant spell once per long rest. The group found the item, then promptly forgot they had it. >.> 
They spent most of the session rigging up some janky Rube Goldberg device, which failed to actually work, and I just told them they could use the item they found earlier. Face-palms all around. 

I think this experience illustrates the whole TTRPG vs video game ordeal. Video games, like Zelda, bake solutions into the mechanics and progression of the game -- if you don't get the hook-shot, you cannot solve the hook-shot puzzles. But with TTRPGs you have to expect out-of-the-box thinking, improvisation, and less "there's only one way to solve this" type problems.   

Here is a puzzle that I created based off of the original Zelda's Lost Woods:

D&D Zelda Puzzle - Maze of the Elements

I'm working on the Water Temple puzzle... I haven't played it, but have gotten a lot of requests to turn it into D&D

Anyways. Hope this helps!

Quote from 1chapelcredit >>

Well, I don't know the answers to your questions... I just know that I'm now going to incorporate at least one Zelda dungeon, room for room, into my current D&D campaign! I'm thinking the Water Temple from OoT...

 

 If it’s anywhere near as hard, your players will hate you forever.

I like your Maze of the Elements. I thought maybe it might be too tedious if it was up to the players to fumble their way through having to fight a million elementals, but once I got to the part of the video with the clues, it made a lot more sense to me. And once they fight one of each elemental, they should have their act together on which way to go.

Quote from TexasDevin >>

I like your Maze of the Elements. I thought maybe it might be too tedious if it was up to the players to fumble their way through having to fight a million elementals, but once I got to the part of the video with the clues, it made a lot more sense to me. And once they fight one of each elemental, they should have their act together on which way to go.

Awesome! Glad you enjoyed it. There were a few other DMs that used a medallion that they gave their players that served as a "compass" on which direction to go.

Good luck! I'm hoping to come up with something for the Water Temple very soon. :)