Jerry was gay. Sugar would have realized that. Besides, she was only attracted to "bad" guys.

SUGAR
wasn't innocent either. At first, she only cared about men's money. By the end, they both fall for each other and realize there's more to life than casual sex and money.

I think at the end Joe had a change of heart. That made him more human and I think he did care about her.

Joe seemed to be more of a opportunist, and he knew how to manipulate Jerry, who was a kind man. He did not like the fact that Sugar was more interested on Daphne that him.
When they decided to masquerade as Women, Jerry decided his name would be "Daphne" and one could tell this was a way to rebel against Joe.
As for the relationship between Joe and Sugar, she had made it clear from the start what kind of Men she was drawn to, so no surprise there at the end when Joe opended up to her, she took him for who he was, she was no stranger to these kind of relationships.
Jerry, kept looking & to be always searching, and perhaps hewithout even thinking about it, found what life always eluded him throughout his life, a life worth living with someone who would love him and take care of him, just as it seems he had feelings for Osgood.
Just my opinion.
"it's a Kafka high, you feel like a bug"