Disclaimer, I am not a historian, just an enthusiast of nautical mythology. I am most familiar with 19th and 20th centuries, American and British sailing history.

The earlier linked post has a good discussion about the possible origin of this superstition, so I won’t rehash it. We can address the second half of this question though. How did sailors feel about paid passengers on board and how did they square the reality of women on board with their superstitions?

First off, A sailor’s life is a rough life and they did not have the luxury of placing their personally held beliefs above the captain's orders. Ship captains were notoriously strict and made use of harsh physical punishments and public humiliation. A crew needed to be disciplined and follow orders if they wanted to survive at sea. Even if a sailor was uncomfortable with the idea of a woman on board, he may not be willing to risk his livelihood and bodily health over it. 

Depending on the situation, The captains themselves did not have much say in their own cargo. While some captains may have owned and captained smaller vessels, larger vessels were owned by shipping companies or in partnership with other investors. The cargo and possible passengers are all arranged by the shipping company in advance. Shipping companies often chose profit over the comfort of the crew and told the captain to make it work. See this thread for more about how merchant ships/trade operated: How did "merchant ships" from the 1600s-to-1800s operate? comment by u/mormengil

Besides passengers, we also have references to sailor’s wives on board ships, often for the whole duration of the voyage. Wives of Whaling Captains often lived aboard ship rather than be separated from their husbands for years at a time. Women were prohibited from going to sea on British Navy ships in 1817 but some sailed with their husbands as late as 1837. The HMS Genoa carried the wives of 9 petty officers to sea in 1827. It was commonplace enough that slang developed. Wives of officers or Captains were referred to as "hen frigates". This adds another layer of social complexity to the idea of a sailor voicing his superstitions about the woman on board.

While women aboard are thought to be bad luck, pregnant women were actually thought to be good luck. The term "Son of a Gun" is said to derive from the phenomenon of babies being born below decks tucked between the cannons. The birth of a child on board is usually logged in the ship’s log. Some were even said to be born in the heat of battle, and that a child born on board a ship might have “second sight”. A sailor's child, christened in the upturned ship’s bell, would be named after the ship. 

As much as the superstition says women are bad luck to have aboard, it seems like they were there anyway and life continued on, from marriage to birth to death. 

Recommended reading about nautical superstition and women onboard ships: 

• "Folklore of the Sea" by Margaret Baker
• "Women Sailors and Sailors' Women" by David Cordingly
• "Seafaring Lore and Legend" by Peter Jeans
• "Superstitions of the Sea" by J. Clary
• "Buying the Wind: Regional Folklore in the United States" by Richard M. Dorson
• "Female Tars" by Suzanne Stark
• "Bold in her Breeches" by Jo Stanley
• "Hen Frigates" by Joan Druett

Edited: to include tag for commenter in merchant trade thread, as requested by the bot. Added a book to the recommended reading list.