I have a question about whether this is a bug or not, but when I obtained Michiku and Dihliya, Hitomi disappeared from my assistants and now she won’t join my team anymore. (I hope to receive a response in the near future.)

You must have reset her quest from Lady Mystery as it happens in reverse. If you have meet Mrs.Yamada/Hitomi in the past and have sex with her you will not have Michiko and Dahlia as your assistants.