Do illness' underneath the current private maid count as in play? Basically we had a private maid with an illness, then Sora Nakachi placed over her. Would Sora's ability work on the illness card underneath her?
[During you starting phase: you may move one Event card from a Private Quarter of your choice to an equivalent place in another player's Private Quarters.]
No. Once something goes down on top, what is underneath is no longer relevant until the end of the game. If they're ill, then no longer relevant even for scoring.
To my understanding, this is not how illnesses work.
While you can only make the maid on top of the Private Maids stack ill, you can in fact cure any ill maid.
Here is a reply from Zimeon (who translated the rules into English) in another thread, safran-virginie-and-illness-questions
If your private maid is ill, you can still hire a new one. You can still remove the illness of the private maid below, but her effect will never happen again if you employ a new one. You can't change the order of your private maids. And while you can cure any illness, you can only make the top one ill.