From Chapter 8:

"But, if I know myself," said he, "this is from no want of gallantry towards them. It is rather from feeling how impossible it is, with all one's efforts, and all one's sacrifices, to make the accommodations on board such as women ought to have. There can be no want of gallantry, Admiral, in rating the claims of women to every personal comfort high, and this is what I do. I hate to hear of women on board, or to see them on board;..."

I take what the Captain says at face value. It can be difficult to make ladies comfortable on board. A short journey to carry women from point A to point B is not an issue. But a longer journey, one that could take months for example, would be a different story. The food is good in the Captain's cabin, as long as he has adequate stores. Generally, he has fine china, silver, etc. and his own cook and steward, but after a long journey, he may wind up eating the same salt pork as the crew. If the ship is far from home or in dangerous waters, anything could and did happen. The ladies would be sent below decks in battle, but cannonballs didn't just hit the top deck and the dangers were very real.

Sophie Croft talks about traveling with her husband, but she never says whether she was on a ship during battle or not. I think if the Admiral were planning to go into battle, he would have left his wife on shore. This may explain why she spent a winter at Deal while he was at sea.