This is yet another tough one, I was planning on replacing modded weapons with their base counterpart. In the previous version we made Burkes silenced 10mm a unique weapon. I had a working setup that made merchants sell mod kits, no where near as widely available as in NV, but they were still around.
In my opinion, weapon mods are the best thing about NV, but it is stupid that they don't work on NPCs. Completely defeats the purpose. But I don't see a solution to that.
Fortunately there are only two weapons that fall into this. The Scoped .44 Magnum is only used by a handful of NPCs, none of which are going to need the scope to snipe at you; the unscoped magnum could easily be used in its place with no issues whatsoever. The Silenced 10mm Pistol is ONLY used by Mister Burke, and I think the method of making it unique was a good idea. It certainly provides a way to restore the increased critical chance that the old Silenced 10mm Pistol had.
Now as far as weapons you find, I had a thought on that: in certain places where you would normally find a Scoped .44 Magnum or a Silenced 10mm Pistol, say in boxes and such, include the weapon and the mod. Not very many - we don't want to be overrun with weapon mods - but a few key locations could be a nice bonus.
As for the rest of the weapon mods, I agree that they are one of the best things about NV versus FO3. We should definitely have merchants selling a small subset of them in the CW, if only the ones that apply to CW weapons.