Evolution. Evidently, any living creature in Mordor has a better chance of survival and reproduction if it has a red eye clearly visible somewhere on its body.
(And if you don't agree, just consider what happens to orcs who fail to display the said eye.
)
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Vanity, or the need to prove, more to himself, that he has complete control over his land and his minions. Loathing of any unspoiled thing or creature, especially within his power. How can he be the Great and Powerful Sauron, the First of His Name, if Eru's flies still thrive on his Orc-dung? I'm joking here, but I think he would have found it unacceptable to leave a single pebble, let alone a living creature, in its pure and clean form. It would have irked him endlessly - he'd feel he doesn't have true dominance and control over it until as little as possible of its original essence remains.