Okay, so I bought two sniper rifles, both mods for each of them, and enough ammo for me an Boone to both use them. So I full mod my rifle, and it works fine, suppressor and all. Then I modded Boone's rifle with both mods, and tested it. Worked fine, suppressor was on it and all. But then I gave it to Boone, but it doesn't have a suppressor anymore, so it makes noise now, making it hard to sneak with him. So I took it away, but for me it still had the suppressor when I equipped it. Can companions not use suppressed weapons or something?

I don't think companions use mods. The only way to give him a silenced sniper is to literally give him a silenced sniper, and I only know of one:Christine's Sniper from Old World Blues

Companions ignore mods on a weapon given to them.

Thanks mate. It's too bad companions ignore weapon mods. I wonder why Obsidian did that.