At no point can you talk to her father, the engineer, and bring up that you met his daughter.
You can. He will simply say that you're mistaken and he never had a daughter, almost certainly because he disowned her for working for oligarchs, the very people he hates more that anything in the world for pretty much ruining his life. I can't think of a better reaction, it's perfect.
Once she is gone, she is just gone. It almost seems like there wasn't enough time and so the story just got cut short, which is understandable with so much other stuff going on in the game.
I don't think of it as unfinished. I think it's much better this way, like less is more in this case. You're right, she's just gone. There's no justice, no closure, nothing. Which makes it hit you that much harder and makes you use your imagination. It wouldn't have nearly the same effect if we just found her body somewhere. This might be a spoiler for you, but did you know that (highlight this if you want to know)
Gunnar Edstrom, the CEO of JKK, is rumored to be involved in slave trade? Knowing that, what do you think might have happened to her? It's just a theory of course, but one you couldn't think about if we just found her body.