Unfortunately, I've discovered that NPCs do not use the mods on modded weapons. I gave Cass a modded sniper rifle, with a silencer and the carbon fiber bits (it was my main gun until I got my shiny new Gauss Rifle) and I noticed that while on Cass, it just becomes a standard sniper rifle. Which is annoying, since I was hoping to have her NOT alert everyone to our presence every time she fires a shot. Oh well, I guess.

There are other companions who're sneaky. Cass, not so much.

But I noticed that as well. I just gave Boone the Gobi rifle and let him go to town.

Yeah. Boone was my go-to guy in my first playthrough... which was fun when I decided I was bored one day and that we should go straight to the Fort and murder our way to Caesar... but he's mighty depressing. Cass drinks a lot and is entertaining.

The only other NPC I've had is Veronica... and while she's great and all, her lack of levelling starts to become an issue later on. Nice thing is... she doesn't use up all my ammo... and she gets extra <3 points for being Felicia Day.

Try giving her a weapon that's already silenced. Like the Ratslayer maybe?

Npc's cant use modded weapons, but can use different ammo types.

I second Enduring Protectron's suggestion. But one companion in particular is meant to be used for sneaking purposes, and anybody decent with melee can function like so as well.