Wide open always refers to the aperture, and it means the largest aperture the lens is capable of (lowest f/#).
Softer picture at f/2.8 or f/16 depends quite a bit on the lens. Many prime lenses are as sharp as they are going to get by f/2.8 and so they will likely be a small amount less sharp (due to diffraction) by f/16. Similarly, some of the top zoom lenses are very sharp even wide open at f/2.8, and so these too might be slightly less sharp by f/16 due to diffraction.
Lens sharpness is dominated by two curves. One is the sharpness of the lens due to optical aberrations. This curve delivers sharper results (less aberrations) as the lens is stopped down. The other curve is softening due to diffraction. This curve gets sharper as the lens is opened up.
Between the two, we usually see a lens that gets a bit sharper until one reaches somewhere around f/8 to f/11. Beyond this aperture the lens will start to get softer again due to diffraction.