Here's my feedback. Please do not change the heroines' names.
Modified Hepburn is simply the superior choice for romanization of any kind. Deciding which kanji to leave out during romanization is a bit ridiculous, like 志衣菜 -> Shina. Yuuka is another case. Yuka and Yuuka are 2 different names in Japanese, so let's not go down the SakuSaku route. While the site is inconsistent with her name, I would think the description was written by the translator, and such reflects the change in-game.
The full list is below, along with the devs' character description links, which include their names and furigana:
Character in question: Hiiragi Yuzuyu
Title: Sanoba Witch
Character in question: Shiiba Tsumugi
Title: Sankaku Renai
Character in question: Kisu Shiina
Title: Hello, good-bye
Characters in question: Hiiragi Koharu, Rindou Natsume
As there's no furigana, here's the game's wikipedia article which
includes it - https://ja.wikipedia.org/wiki/Hello,good-bye
Title: Melty Moment
Character in question: Orie Yuuka
Character in question: Bonus - Hiiragi Chiemi (I know you didn't write her description, but considering the fate of the other two characters with this family name, I'm adding her too.)
Thanks for not giving me cancer.
PS: Yes, I know I didn't mention Shuuji (one of the MCs). I don't care about guys' names, but you could change it back as well. You know, for consistency.