I like to think that the Medusans exist in a different way from what we consider 'normal matter'. They have bodies sure, but they exist in a phased state that causes the humand mind do go mad when trying to perceive it. Kind of like an extreme form of sensory distortion (i.e. hearing from your eyes). Or as another example, 2001's images in the end are things that aren't really there, but they are the closest things that Dave could comprehend. The visor perhaps filters out some of this, or blobs the vision whenever certain wavelengths that defy humanoid perception hit the screen.
It's not any fault of the Medusans, obviously, but life and matter evolved differently on their world.