The eyes aren't real. They glow, yes, but this is to scare of predators. This is also how they are used when Kabuto is on the sea floor. They do not help Kabuto to see in any way.The Pokédex would disagree with you on that. Kabuto's Yellow Version dex entry reads; A Pokémon that was recovered from a fossil. It uses the eyes on its back while hiding on the sea floor.
And its Crystal Version dex entry reads; Three hundred million years ago, it hid on the sea floor. It also has eyes on its back that glow.
Not only do these tell us that the eyes on top of its shell are real, but Crystal also strongly implies that those aren't its only eyes, meaning that the red ones we usually see are real as well.