Harley doesn't see attractiveness in the same way as other people. She flirts with people who she is attracted to on a mental and social level, and it is not just about 'physical appearance'. So even though Thor does not feel he is attractive right now -- Harley is going to still flirt with him. It is part of her personality.

"I worked in a hospital, ya'know. So I do have experience if you wanna assistance." During her time in Arkham, there were many patients who had to be dragged to the showers. But Harley doesn't want to do that to Thor.

She flips the omelette, starting to cook the other side.