You have checked that the surface of the glass is clean. Discounting water staining or the effects of burial (which are chemical effects), the only thing that will affect the colour of glass beyond the surface is UV light, but only IF the glass formula contains manganese. It was probably an inferior glass batch
The only things smoke free is important to are textiles, paper, leather, and porous surfaces, etc. that will actually absorb the smoke, and things that cannot be washed. Have you ever seen clean window glass that was yellow?