There are two bugs that both cause this issue.
While this usually has no effect, it can sometimes completely remove the crafting tab.
1: Hammer Bug (https://pastebin.com/mMdn0QV8)
2: Loot table for mana sieve is unable to parse without Botania installed (https://pastebin.com/Zq8CkSDH)

Tested on Minecraft 1.16.5, with only the latest versions of JEI, Ex Nihilo Sequentia, and Ex Compressum installed.

To reproduce:
1: Install the mods listed above.
2: Enter a world.
3: Check latest.log.