When creating a new world with the config already present, the disabled features still gets shown in JEI.

{
  "version": 7,
  "FoodItems": {
    "FriedEgg": false,
    "BerryPie": false,
    "HoneyedApple": false
  },
  "WateringCan": true,
  "RoseGold": false,
  "Ropes": true,
  "EnchantmentPrecision": true,
  "EnchantmentSpeed": true,
  "Wrench": false,
  "CopperPatina": false,
  "AmethystLamp": {
    "enabled": false,
    "despawnChance": 0.5
  },
  "Crossbows": true,
  "TridentShard": true,
  "GlowStick": false,
  "GildedNetherite": true,
  "DepthMeter": {
    "enabled": true,
    "displayElevationAlways": false
  },
  "MysteriousBundle": true,
  "CompostableRottenFlesh": true,
  "MusicDiscs": false,
  "NoteBlockAmethystSounds": true,
  "ShipwreckSpyglassLoot": false,
  "PocketJukebox": false,
  "ChickenNugget": false,
  "PoweredRailsCopperRecipe": false,
  "GoldRing": false,
  "GlowBerryEatGlow": {
    "enabled": true,
    "duration": 5
  },
  "HastePotions": true,
  "BundleRecipe": false
}

While not craftable and are without any recipes, the disabled items are still shown.

When clicking on certain items (like those which are enchantable) the usage of anvil applications can show up.

Disabled features also present in creative menu.

When some of these items are disabled, it is very likely expected that they wouldn't be visible from NEI , REI, JEI, etc. nor the vanilla creative menu.

I can't hide them from the creative inventory unfortunately, but I'll see if I can hide them from jei/rei/nei

I've seen different mods conditionally register items based on it's config. Would something like that be possible?

Doesn't the item automatically get removed? I'd imagine it's the same as if someone installed a mod and used its items in a world and then removed the mod and joined the world again. It normally just removes unknown registered items I believe.

it is possible, but then if you disable something and try joining a world which had this previously enabled, the world won't load, so that's why I won't do it

it is possible, but then if you disable something and try joining a world which had this previously enabled, the world won't load, so that's why I won't do it

But from what i remember this is actually a minecraft bug, so in theory it can happen with any mod. So i don't think you should have to be that careful (and actually add stuff conditionally, like the other user said)

as of 1.20 i think i can remove things from creative inventory now, will look into that