Unless you tell Blender to do otherwise, it simply uses the first material slot for the object, so if the glass is further down, it won’t show.
That’s another good way to shrink the glass, absolutely.
I don’t apply the rotation very often, unless I want a specific default rotation and/or work with modifiers that rely on rotation. In the case of the shelf pins it doesn’t make a difference whether the rotation is applied or not, so I leave it alone.
If I were to apply an array modifier to them, I might revisit that decision.
