"It?" Will probably looked like a scared little bunny at that moment, what did Jack mean with it? Sex? He wasn't wondering about that, was he? No, he had been wondering what Jack been thinking about. Was Jack thinking about sex? Probably...
He might be immortal now, live for ever and all that but when it came down to things of the heart he was still that boy that was rescued from drowning by Elizabeth. He had never looked at anybody else and now he was there with Jack thinking about sex, not just any sex, but sex with Jack.