I installed both upgrade aquatic and aquaculture 2 (https://www.curseforge.com/minecraft/mc-mods/aquaculture), but the loot tables overwrite eachother, so you only get items from upgrade aquatic, and not aquaculture.

I too am seeing this issue with Tombstone. None of the Tombstone special drops from fishing occur when Upgrade Aquatic is installed. I confirmed they still drop with only Abnormals Core installed. I tested without Optifine as well and the only fished drops are from Upgrade Aquatic.