Okay, hear me out, from what we knew about her whereabouts during all endings, there no way for her to die in secret ending. Let see:
In “devil” ending, after making decision during the night, we go to her mansion by next morning, and later arrive with her into arasaka tower during board meeting, where she try to oust Yorinobu. At this moment his guards attack everybody here. While he later claims that he didn't want to kill her, and locked her in the mansion for her own safety (he seem to be sincere), by this point he had no choice.
In Rogue and Panam route we spend entire day preparing for assault, and by that point aforementioned meeting should already be over. So, either she was killed during that meeting, or she was in the tower during assault and was killed by Alt.
In secret ending we don’t wait, and attack Arasaka tower that very night. Which mean by the time we finished, Hanako should still be in the mansion. And by morning Mikoshi was gone, and with it her only real chance to overthrow Yorinobu. She doesn’t seem like a person to commit seppuku, and she’s cunning planner. It’s unlikely that she would get herself killed any time soon.
P.s. on related note, Takemura have exactly the same message in all ending where we go against arasaka. I would argue that singlehandedly assaulting arasaka tower should earn at least grudging respect. Maybe even some special, more friendly, variation unlocked by right dialogue choices.