I’m just stating some explanation that I told myself while reading this story, so the story would make more sense:
Chen Yu is under 18, so he could be a late bloomer, so his masculine features haven’t been showing yet, but more child-like, girlish look.
Chen Yu is probably received no education ( dirt poor) and a kid who live with a mom, so he may not know much about different gender genital. Plus, Uhm that family probably cut his thing ( 😬)
The prince, Zhen Bei could be gay n sexual frustration, part of the reason he is so cruel n sexual compatible, lead to Love our pitiful Chen Yu.
Zhen Bei probably already figured out Chen Yu is a boy, but not saying anything n also hide that fact from everyone else.
This story setting was in way back when high social position people had absolute power over people like Chen Yu (servant, disability)
Chen Yu was bullied and abused since he was born, plus the society n environment he lived in. Zhen Bei is the only one consider good to him besides his mom.