This Wall Street Journal article from back in 2013 answers some important questions about whether reading in dimly lit conditions or reading on a device like an iPad or phone can actually cause damage to your eyes. It turns out there is no evidence of long-term damage or change in the physiology to the eyes but it may cause discomfort or fatigue.
However, the lead is buried in the last paragraph of the article and explains why pirates wore eye patches:
“Ever wonder why a pirate wears patches? It’s not because he was wounded in a sword fight,” says Dr. Sheedy. Seamen must constantly move between the pitch black of below decks and the bright sunshine above.
Smart pirates “wore a patch over one eye to keep it dark-adapted outside.” Should a battle break out and the pirate had to shimmy below, he would simply switch the patch to the outdoor eye and he could see in the dark right away—saving him 25 minutes of flailing his cutlass about in near blindness