I also verified against a new npc, and dragging the assault rifle to the inventory, and dragging the smartgun link to the assault rifle weapon mods appears to show up as expected. So it might've been a fluke when copying it over. If you open the smartgun link from the items list, and verify there's an effect there under the weapon bonus input, there should be something there. If there's not, I'd recommend unloading the module and reloading it.