Yeah. I think that demarcation, where you can't have spoils until some event, isn't advantageous, it doesn't add anything to the game. I didn't ever really like the spoils bag in Wind Waker. It wasn't bad, it just didn't add anything. It's not like Link is carrying around a hammer, a shield, a giant Deku leaf, a hookshot, a bow, etc. and then he's like, oh a feather from a Kargaroc? Where am I going to keep this!? With your other stuff, obviously.
Anyway, in organizing these items into the menu, I think something we should straighten out is how these items are consumed. Can you assign a green chu chu jelly to a button? Or any other spoil? Would that serve a purpose? I think the purpose of the spoils bag was because you could assign the spoils to a button like you could the bow or hookshot.
For the enemy drops as far as I know (chu chu jelly, Poe souls, potentially seashells?), there isn't any point to making them usable of the player's own volition. So I think that the only way they can be used is prompted. If you're talking to the potion shop owner, he'll prompt you to give him chu chu jelly. It doesn't really need to be assigned to an item button.
This is an important distinction because it means we don't have to put these items on the item selection screen of the menu. We could keep their quantities listed is a section of the quest status screen, where heart container completion percentage, flippers, etc. are shown. Or even its own page or popup box (basically the spoils bag system, but not assignable to buttons), because we seem to have a lot of different colors of chu chu jelly.
Lol, I feel like my science writing classes came out in this post. Tl;dr version: we should have the enemy drop items like this just listed as quantities on the quest status subscreen. Or maybe their own subscreen. Like,
Poe Souls: 6
Green Chu Chu Jelly: 2
Red Chu Chu Jelly: 4