Since they are not really "Engrams"
The only way of disable the artifacts, is to make it so that crafting a artifact, costs the same artifact as you want.
That way it's not possible to craft them

The code below is excample of making the artifact of depth, cost the same to craft:
Put it in your Game.ini file

ConfigOverrideItemCraftingCosts=(ItemClassString="Artifact_AB_Depths_C",BaseCraftingResourceRequirements=((ResourceItemTypeString="Artifact_AB_Depths_C",BaseResourceRequirement=1.0,bCraftingRequireExactResourceType=false)))

Artifact_AB_Depths_C
Artifact_AB_Lost_C
Artifact_AB_Shadow_C
Artifact_AB_Stalker_C
Artifact_Brute_C
Artifact_Clever_C
Artifact_Cunning_C
Artifact_Devious_C
Artifact_Devourer_C
Artifact_EX_Chaos_C
Artifact_EX_Growth_C
Artifact_EX_Void_C
Artifact_Hunter_C
Artifact_Immune_C
Artifact_Massive_C
Artifact_Pack_C
Artifact_SE_Crag_C
Artifact_SE_Destroyer_C
Artifact_SE_Gatekeeper_C
Artifact_Skylord_C
Artifact_Strong_C