Currently (Apotheosis 8.3.4 in Minecraft 1.21.1, Craftoria 1.20.3), shift-clicking the output of a malice recipe in a smithing table does not apply malice properly; the resulting item stack still has the "Malice will be applied on craft" line and no malice is actually applied.

Clicking the output slot normally to put the output item in the cursor applies malice properly.