Usually this happens when a mod hard-codes the drops in some ways. (Neo)Forge "Global Loot Modifiers" are an example, or BcLib block drops (at least in the past)

So, the best way to show loot is replace loottables directly / entirely?
I tried to use global loot modifiers and it quite convenient to not override a whole loottable, but then it doesn't show loot in EMI Loot.

long delay to respond, but yes, either replace the loot table, or I hear that LootJs now properly ties into loot events and can be seen by EMI Loot. LootJs probably offers mechanisms for "bulk" modification a la GLMs