It's been years since I've actively studied anything related to the Age of Sail but once a fangirl, always a fangirl, I suppose. So, to answer your question, women were considered bad luck on ships because they were believed to be too physically inferior to be of any use in actually sailing the vessel while also distracting the men on board and leading them into acts of vice. If the men were distracted from their duty to the ship in this way and therefore failed to sail the vessel properly, it would anger the stormy sea gods who would then punish the entire ship with rough seas and bad weather, possibly even causing the ship to sink with all hands on board.

Such beliefs often had dire consequences for women aboard ships at sea. In 1379, Sir John Arundel set out for sea in support of the duke of Brittany but stopped on the way to violate a convent of nuns, even allowing some of his men to take some of these women with them out to sea. The fleet ran into heavy storms off the coast of Cornwall, though, and thinking that it was the fault of the women on board, the crew threw them overboard. (See, The Chronica Maiora of Thomas Walsingham (1376-1422), ed. and trans. by James G. Clark and David Preest (Woodbridge, 2009), pp. 96-99)

Yet, paradoxically, women were believed to be the best navigators and the presence of a naked woman was thought to be good luck at sea, hence why a number of ships' figureheads were bare-breasted female figures. It was thought that her open eyes would lead the ship to her destination while her bare breasts would shame the sea gods into calm. This effect of female nudity over nature was recorded by Pliny in his encyclopedic Natural History (Book 28, Ch 2) where he wrote that a menstruating woman who uncovers her body has the ability to scare away hailstorms, whirlwinds and lightning. If she walks naked around the field, caterpillars, worms, and beetles will fall off the ears of corn. And, even when not menstruating, a woman can still lull a storm out at sea by stripping down to nothing.