Why Did Pirates Wear Eyepatches?

The fact that some pirates wore eyepatches most likely had nothing to do with a missing eye, and everything to do with being able to see - specifically, above decks and below them.

Pirates frequently had to move above and below decks, from daylight to near darkness, and the smart ones wore a patch over one eye to keep it dark-adapted outside. When the pirate went below decks, he could switch the patch to the outdoor eye and see in the darkness easily.