Is there any option to blacklist specific items that will not be equipped with gem slot after crafting the item?

I'm asking because in some mods (e.g. MineColonies ldtteam/minecolonies#9100) there are quests which are requesting wearable items and it is impossible to complete them.
I believe it's caused by adding NBT data to the item by adding socket slot.

So if there isn't this feature I think it would be nice to have it in the future.

I'm not sure what you are referring to. Apotheosis does not apply gem slots to freshly crafted items, only those generated from loot or those reforged using the Reforging table.

That's strange because when I craft something it has gem slot by default. Even when I'm looking at it in JEI.

Isn't that socket from https://www.curseforge.com/minecraft/mc-mods/passive-skill-tree?

Apotheosis should be grey

Interesting, that could be it. I don't have that much knowledge about other mods so I thought this mod adds sockets for its gems.
I might check that mod you mentioned instead.
Thanks for clarification.