I use JeiTweaker to hide items from JEI. I am trying to hide enchanted books from the item index.

Normally, using JeiTweaker works perfectly fine. However, when an item with an NBT, EMI will hide all items with that nbt. This not the case with base JEI; only the item with the specified NBT will be hidden as usual.

The semantics for something being hidden in JEI and how that translates to EMI is not very clear, there is some rudimentary attempts to forward hiding, but ultimately if you want something precise you should use EMI's dedicated hiding features.