To put it in perspective: when they visit each other, they share a bed. Snow Flower always cups Lily's cheek until they both fall asleep. There's one instance where they're half naked, staring at each other, and end up drawing words on each others' stomachs. The narrative even makes note of small details Lily explains are erotic, and Snow Flower spends some time staring at Lily's breasts.
The reader's group guide in one edition of the book even invites you to speculate on their possible sexual relationship.
Nightmare Fuel and Nausea Fuel: The detailed descriptions of Third Sister's blood poisoning and Beautiful Moon's death by anaphylactic shock are...unsettling. Footbinding itself takes a starring role in the early part of the book, visited upon five and three year old girls, no less. The fact that the narrative shows how important and accepted footbinding is only heightens this discomfort.
The Woobie: Snow Flower, full stop. Lily also qualifies, especially when she comes to regret the misunderstanding that tears them apart.