I'm running fabric on 1.16.5, and items don't get their nbt data when crafted, as well as nbt data isn't checked for ingredients.

Here's the piece of code I'm using:
event.replaceOutput({}, 'minecraft:diamond_shovel', Item.of('minecraft:wooden_axe', {Damage:0,Enchantments:[{id:"minecraft:sharpness",lvl:1}]}))

Result in game:

Afterwards, I tried copying an example from the wiki and putting it in my code:
event.replaceOutput({}, 'minecraft:diamond_shovel', Item.of('minecraft:enchanted_book').enchant('minecraft:respiration', 2))

And in game it still has no nbt data attached:

Fabric / Vanilla doesn't support NBT output in recipes by default, you will need to use other mods (like NBT crafting) to potentially re-add support for that.