To my knowledge yes and no. Quite a few pirates, I'm sure, did injure their eyes during boarding and fighting due to the immense amount of wooden shrapnel that was common in naval battles. But from what I've read, and know from contemporary naval armies, the most common use of eye patches was that covering one eye made the eye retain it's night sight. Below deck there might have been a few candles lit but in the armoury and provisions hold it was strictly forbidden due to the volatile nature of black gunpowder and general fire hazard. Never the less a few candles won't illuminate a whole lot and since candles in that age was made from tallow that both smelled bad and produced a great amount of soot it was a far more efficient way in that you covered one eye with a patch to see in the relative dark below deck.

Source: Amateur historian in contemporary Swedish naval warfare.

Ana de Mendoza is a great example of someone wearing an eyepatch in the 16th century. There are a few portraits of the Princess out there.