I have been following some of the achievement discussions, and while I don't have a solid answer, *most* mods should not do that, *but* people are still arguing over what you can do and still have achievements.
I don't get them at all because the Steam Overlay crashes my game, so I had to turn it off. Someone else said they still got achievements, I think they were confusing offline mode with the overlay.
People are still arguing over whether console commands disable achievements. The only way to be sure is try it and find out.
It would help if you posted the name of the *specific* mod.