I'm curious and slightly confused. Are the eyes the lines on the bone like mask (I really don't know what that is), or the red dots. On multiple sprites, it is shown that they are on both sides of it's face. Same for Kabuto. Are the eyes the black dots on top, or the red ones at the bottom?
Relicanth:
...there is a red spot located on both sides.
Bulbapedia probably would have said "eyes" instead of "red spots" if they were in fact eyes.
Kabuto:
There are two small, black eyes on top of its shell, which it uses for sight when it hides on the ocean floor... second pair of luminescent red eyes are visible on its underside.
Source
Kabuto has two sets of eyes -- the ones on top, and the ones under the shell.
Hope I helped!