Why are we unable to see/perceive atoms on or inside the eye. How do the atoms of the lens not obstruct the view of the pupil? Or what about atoms or cells inside the pupil that are even closer to the RGB cones?
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Individual atoms are much smaller than visible light waves. The result is that they be ‘seen’ by visible light, as it mostly just passes around them.
On top of that, many atoms do not absorb light at all. Certainly the ones in the lens and fluid of the eye. Water, for instance. The light does slow down passing through, but it does not get stopped, so it does not create a shadow.
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