Most quest items aren't even kept in your bag, they just exist on their own limbo. Ones that need to be used are but can be used directly from the quest list itself and then its removed from your bag when the quest is done anyway, meaning its position in your bag is meaningless.
Heck even in Vanilla they made a separate keyring bag just to keep keys in because those were intended to be quest items you needed indefinitely.
Also, OoT is a bad example of the problem unless you are making that exact type of adventure game instead of an RPG. Because all the "quest items" are just plot coupons with no actual "use" in game. You could replace the screen with just a white checklist and accomplish the same function. Especially as once the main quest items are acquired, they will cease to matter whatsoever anyway, outside of narratively. They only serve as a check that you've finished a temple, as every single one is tied to a boss kill sans the freebie Light one. I'd say its redundant in fact to have them at all.
In fact, the original N64 version's most famous flaw was directly designed to a failure of its inventory system. Which was the constant need to pause and equip the Iron Boots, which the long lag each time making it feel like forever. This was fixed in the 3DS version, but the whole reason the flaw existed was the design choice to separate "items" from "equipment" originally leaving your equipment unable to be assigned to the C buttons.
Those are nitpicky complains about the game of course (except the Iron Boot one), but its a nitpicky topic. And I play an OoT randomizer like once a month so I know an autistic amount about the game.
Speaking of OoT rando, it does have one "undroppable" quest item: Ruto's letter, taking up a bottle. It's not actually relevant in vanilla, being so close to where you turn it in, but it might be in rando, since you can theoretically find it without access to King Zora.
Even then, probably not all that relevant. I don't remember if you can get blue bottle off of it, but if you can, then that's 90% of the use of a bottle right there.
It does in fact sit unusable until you can access King Zora with either Zelda's Lullaby or the Scale.
Fortunately, the only hard requirements for a bottle are also behind King Zora. Being the fish for Jabu and the Blue Fire, and I think a single or double use in Ganon's Castle if you have to do the Water Trial (which by that point if you don't have a bottle you are really unlucky). The only other checks the bottle opens up is the bugs in bean patches for 9 additional Skultula checks, which is a setting most people don't play with anyway.
I did forget the single "usuable" quest item slot that is designated for the Chicken/Letter, but that only exists to show off the day/night cycle and both are one use anyway.
Amusingly, WoW figured it out a while ago.
Most quest items aren't even kept in your bag, they just exist on their own limbo. Ones that need to be used are but can be used directly from the quest list itself and then its removed from your bag when the quest is done anyway, meaning its position in your bag is meaningless.
Heck even in Vanilla they made a separate keyring bag just to keep keys in because those were intended to be quest items you needed indefinitely.
Also, OoT is a bad example of the problem unless you are making that exact type of adventure game instead of an RPG. Because all the "quest items" are just plot coupons with no actual "use" in game. You could replace the screen with just a white checklist and accomplish the same function. Especially as once the main quest items are acquired, they will cease to matter whatsoever anyway, outside of narratively. They only serve as a check that you've finished a temple, as every single one is tied to a boss kill sans the freebie Light one. I'd say its redundant in fact to have them at all.
In fact, the original N64 version's most famous flaw was directly designed to a failure of its inventory system. Which was the constant need to pause and equip the Iron Boots, which the long lag each time making it feel like forever. This was fixed in the 3DS version, but the whole reason the flaw existed was the design choice to separate "items" from "equipment" originally leaving your equipment unable to be assigned to the C buttons.
Those are nitpicky complains about the game of course (except the Iron Boot one), but its a nitpicky topic. And I play an OoT randomizer like once a month so I know an autistic amount about the game.
Speaking of OoT rando, it does have one "undroppable" quest item: Ruto's letter, taking up a bottle. It's not actually relevant in vanilla, being so close to where you turn it in, but it might be in rando, since you can theoretically find it without access to King Zora.
Even then, probably not all that relevant. I don't remember if you can get blue bottle off of it, but if you can, then that's 90% of the use of a bottle right there.
It does in fact sit unusable until you can access King Zora with either Zelda's Lullaby or the Scale.
Fortunately, the only hard requirements for a bottle are also behind King Zora. Being the fish for Jabu and the Blue Fire, and I think a single or double use in Ganon's Castle if you have to do the Water Trial (which by that point if you don't have a bottle you are really unlucky). The only other checks the bottle opens up is the bugs in bean patches for 9 additional Skultula checks, which is a setting most people don't play with anyway.
I did forget the single "usuable" quest item slot that is designated for the Chicken/Letter, but that only exists to show off the day/night cycle and both are one use anyway.