Yes. Lenses does affect the image quality. It would be absurd to say that lenses does not affect image quality. If that were true why would people pay thousands upon thousands of dollars to get premium lenses?

Quality premium lenses do affect image quality. They will give you sharper pictures and render your image with more contrast.

Talking about Sony DSLRs and Carl Zeiss lenses, have you ever looked through a Zeiss lens? The first time I looked through a Zeiss lens, I immediately noticed the color difference that the Zeiss lens produces as compared to a kit lens. That is merely by peering through the viewfinder. When taking pics I noticed that certain colors tend to pop out better using a Zeiss lens.

Other than that premium lenses also gives you better CA and flaring controls and will mostly offer better bokeh. Thus using the same body with different lenses will affect your output to some extent.

It's always better to pair low end body with premium lenses than to pair high end bodies with cheap kit lenses.