This is based on communications between Asian readers of light novel and mangas
Lily is commonly used to represent purity, innocence, especially in Asian religions. Lily in this case symbolizes tight and pure friendship between 2 females. They can be very close friends to the point of slightly flirtatious or look almost like couples but not necessarily sexual. It's more on the emotional bond rather than the sexual aspect that the West depicted it as.
It's not too common as a visual indicator but more as a genre/category of anime/manga/light novel. It started with 'Rose Clan' as a term for gay inclined readers of a magazine series so a writer start using 'Lily Clan' as a female counterpart t
threads & similar discussions:
From history point of view:
Among the first Japanese authors to produce works about love between women was Nobuko Yoshiya, a novelist active in the Taishō and Shōwa periods of Japan. Yoshiya was a pioneer in Japanese lesbian literature, including the early twentieth century Class S genre. These kinds of stories depict lesbian attachments as emotionally intense yet platonic relationships, destined to be curtailed by graduation from school, marriage, or death.