It strikes me that young women were in a real double-bind situation.

If your behaviour towards a man could be remotely construed as encouraging then you were liable to be censured. If your manners were calm and uninviting this was interpreted as very proper maidenly modesty, and you were liable to be corralled into marrying the dolt!

This sort of nonsense cannot have made matters easier for men (unless we are to suppose that a man would really prefer a wife who was totally indifferent to him or perhaps loathed being in the same room as him).
I have to wonder if Miss Maria Ward's impenetrable calm just looked like perfectly proper female behaviour to the young Sir Thomas, who thereby had no means of knowing that she was in a state of perpetual near-coma. But perhaps her beauty was all he required, and he didn't actually want a wife with emotions or functioning brain cells.

It is hard to imagine the eldest Miss Ward behaving in such a way. Even if her manner was not unbecomingly inviting I'll bet she failed to conceal the fact that she had opinions - another type of female behaviour which was seen as taboo. Could this be why she failed to marry as soon or as advantageously as her sister Maria?

Looking at how Fanny responds when Henry declares his affection, which you quote in your post, it is indeed not surprising that he would interpret her response as encouragement if these sort of rules about proper female behaviour were colouring his perception.