Metroid games have things like the missile and health expansions where you don't need even close to all of them but they're a nice reward when you do find them

Difficult question.

There are obviously thousands of games which don't suffer this problem because they just aren't of a genre which even has any concept of items or searching.

Where it gets interesting is examples where games could suffer it but don't.

I looked through my steam list for an example and one which jumped out is Prey, a first-person RPG shooter.

Prey does have lots of secrets and things to find, but the game also makes it very clear early on that you can always travel back and forth between any area on Talos 1, the space station where the game takes place.

By virtue of this design choice, you don't feel compelled to be absolutely meticulous in your searching because you know you can always return to look again, and cannot permanently miss anything.

Yep, FromSoft makes a lot of intentionally bad and player-hostile design choices (especially when it comes to bonus/hidden/secret content) and their fans love them for it.

Goes under Sen's Fortress instead

I do play with a wiki on the side most of the time (not rn as I'm doing SOTE for the first time) but even then taking a quick 3-7 month break mid-playthru shit like this happens easily :D

Don't know if you'll jive with it but usually with RPGs I'll do a blind first playthrough then in a month or two I'll go back and do a playthrough with a simple flowchart checklist to get all the content. Unless it's classic Fallout, I don't need the checklist anymore, now give me a minute so I can forget the Khan's and Klamath exist.

I need to save the Soulslike storytelling greentexts.

The ones about how you need the random item to make sense of the plot for a specific boss "Lord Brambles : Noo, not my gwimblies"

And sometimes you probe the path "for a bit" and the cutsceme starts locking you in

And then you have the witch quest line that needs you to go to the Plateau before doing some other progress (I no longer remember what is what well enough)

Which is fun for a player aimed at multiple ng+ runs in a row, but a disaster for a player who would have loved to play through some story and may never even know it was there (yes, the girl with eyes of Shabriri, I am looking at you)

There is "exploration", and then there is "obsessively grinding sidequests". If you tie endings to the latter, that is ... questionable design, especially when it's not clear if you're merely pursuing a sidequest or doing something that will lead to a completely different ending.

It is good design only if it's good. The prevalence of Indy games in modern gaming culture has taught me that games should stick to what they do well. If exploration is a meaningful and engaging element it can be excellent. Most of the time in RPGs it's a drag. And even if you don't like it, the influence on the parts of the game that are good means you can't skip it. In an RPG, collectables is something I never interact with because it's boring. I am however getting every usable item there is even though I don't enjoy doing so.

We've taken the largest map in video game history and hidden 1000 needles around it

I dont think they are advocating dropping side content, but instead saying that having side content that is hidden or has no direction can take fun out of a game. For example, in OG pokemon games there are "hidden" items that have no hints or clues that they exist. If you walk to certain spots and press the action button you can find hidden items, but since there are no clues or indicators that they are there, it encourages just walking around and mashing buttons for the entire game in case there is another hidden item, which is the opposite of fun.