Just since it was mentioned that it would be good to have it in a more permanent form than chat I'll mention what I consider is good practice. I'll note that I'm by no means perfect so I'm sure what I've written can be improved

A lot of it is what I would consider "fairness" that means that a player should be able to reasonably do it without outside/dev knowledge. Just to give an example of each I'll give an example of a fair and unfair case.

Unfair: Player has to type "Shroud is the best" on an altar to get a key"
Fair: Player finds a book that states that if you go on an altar and type "Shroud is the best" you'll get a key.

The key difference is that in the unfair example no player would be reasonably expected to type "Shroud is the best" on an altar. However in the fair case the player has found a book with instructions and followed it that a reasonable player can be expected to do without any outside intervention.

So what are the best practices in my opinion?

1. Keys should be located relatively close to the place where you need to use them. If the key is located further away (e.g. DT/GT, JC/HM etc) then there should be lore and clues to strongly indicate to the player that the key is elsewhere and it's likely location.
2. Clues should ideally be available from more than one source. For example it could be rumours, random drop book, NPCs and even magic mouths or signs/map features (e.g. a corpse in GT with diary saying that after slaying the Demilich Master and Arch Wizard of Moroch in DT he discovered that discovered they were sent from GT and entrusted with something). The reason to have more than one source is similar to network redundancy so that if it's only available via a random drop book then in theory a player might be unlucky and not find it that means a fair map is unfair for that player. It also means lore is more comprehensive so it's not just hearsay from a random source a player might not find naturally.
3. Keys should ideally be obtained through "normal" gameplay. So for example if a random generic mob drops a key with a 1/25 drop rate and it's in a location where you're not likely to kill them more than once then it generally cannot be obtained via normal play. However if it is a boss mob at the end of a dungeon then a 1/25 drop rate could be viewed as more reasonable as that mob would be likely to be killed more often but for a random mob a 100% drop rate is more appropriate.
4. Keys should ideally be weightless as players carrying dozens of kg of one-drop keys isn't really great from a player quality of life viewpoint.

Actually the reason keyrings of holding isn't as good is because of the way bags work. For example a key ring can only hold 4.5kg. This means that assuming a key is 0.1kg you have a limit of 45 keys. In addition there is also aspect that it merely reduces rather than eliminates the weight so a 70% reduction means you still have 1.35kg of weight plus the key ring. Further to that it also means that non-standard keys (e.g. chipped pearl in UC) can't be placed within it. Keyrings and pouches (gems and money) seem rather redundant as items as they have a low max carry capacity and heavy restrictions on what can go in them while a rucksack has a much higher max carry capacity and can contain anything. Either way the issue is that having multiple keys etc gives players a cluttered inventory and can potentially add a lot of weight. Maybe a better long term solution is to have something like "key items" that are weightless and appear in a separate inventory.

Well a classic example of a bad key is Raas on the bridge in Countryside called Bridge Keeper. It occupies literally 6 tiles with teleporters on either side. Logically you would kill it and move on as there is no reasonable reason to remain other than to wait for a respawn. However that mob actually has a 1/10 drop rate to open a gate on the other side of the teleporter. Pagoda is also quite bad with a lot of 1/25 drops where key is required to progress.

GT - The keys in DT I believe drop 100% of the time. Orc Necromage key isn't great as mob only appears at night so timing can be an issue. Fire Giant key can be luck based as I believe drop rate isn't great. Raas key I found dropped easily but Lom key has a low drop rate. I guess whether to have access to the short cut is worth a grind is a judgement call.

JC - I've not done JC much but I think the Skelemage Queen doesn't have a 100% drop that is inconvenient when awaiting a respawn.

I'll add that currently I don't think there is any need to move any keys although alternative locations could be more appropriate. Some of them might need to get supplemental lore to justify their locations.

An additional thing I'll add is that if you want to have an overriding theme for parts of the Shattered Planes then having keys and dungeons intermixing could be an interesting way of working the storyline. Let's say that for example you have a storyline where King Rhun has two trusted subordinates who run the Pilfered Mine and Catacombs and only they can grant you access to him then completing those two dungeons could be a prerequisite to getting to him. I'm not saying that specific idea is necessarily a good one but I'm more illustrating the concept that you could have a storyline that spans several dungeons and completing one gives you something to start on next one.