Erin McCarthy says it's NOT because they lost an eye:

Jim Sheedy, a doctor of vision science and director of the Vision Performance Institute at Oregon's Pacific University, told the Wall Street Journal that while the eyes adapt quickly when going from darkness to light, studies have shown that it can take up to 25 minutes for them to adapt when going from bright light to darkness, which "requires the regeneration of photo pigments."

Pirates frequently had to move above and below decks, from daylight to near darkness, and Sheedy says 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 (potentially to fight while boarding and plundering another vessel).

NOT ALL😉