If NPC's have modded weapons, that you can loot ~why bother modding them yourself when they can be found on dead enemies?
Modding will [possibly... hopefully?] be a reflection of PC ingenuity, unless its so commonplace as to be taken for granted in the world.
(like having insanely advanced military stims for healing, instead of first aid kits.)
Mods aren't created from scratch by you, you find them in the wastes and buy them from merchants. If a merchant sells them, it would make sense that they would use one on their own gun?
for sure higher ranking BoS and other fancy NPCs should use them, and maybe a few named enemies and important people. And maybe if like one raider per group had a small chance of having a gun with a mod, since that raider would be the alpha and get all the sweet loot.