Some blocks have been hidden in JEI may cause confuse

But removing these recipes is much easier than tweaking drops

So? Hidden items still show crafting recipes/furnace recipes as well

I guess removing the blocks from the recipe list would be more confusing for many people.
Edit: so what do you want? removing the recipe if the input block is hidden or removing any hidden blocks in the output?
Edit2: did you ask mezz to make hidden items invisible in recipes as well?

I am making a modpack and I plan to completely replace vanilla coal ore with Geolosys‘, but the problem is the previous recipe still shows so I guess it may confuse players.

1. Removing the recipe if the input block is hidden
2. No I didn't because I can simply remove a recipe by using CraftTweaker. But for drops it is more difficult to tweak drops and wasting time investigates hidden blocks seems unnecessary.

There is another solution: adding a blacklist for specific blocks

what? can you explain more precisely?

JEI has an edit mode to hide an item. Hidden items still show the drops

It's not that difficult to remove drops from the list. open config/BlockDrops/blockdrops.txt, search for 'coal' and delete the entry.
I don't know if it is possible to hide recipes dynamically

Thanks that will help.