I've seen and experienced everything mentioned except for the smoking corpse but never piece them all together, good job! As for Vivian ghosting I don't think that's the case because Ola wouldn't react/talk to you the way he did when you asked about Vivian.
My theory is he (or somebody in JKK, but he's in on it) rigged that floor grate to collapse when somebody stood on it, and it was right in front of the lever needed to turn that thing on. Vivian was suspected of being a spy, and since she's a known mechanic (Mykola is a mechanic, like father like daughter), they could send her to "fix" it (probably they rigged whatever it is to be broken in the first place). Is there anything in-game that makes you think Ola/JKK even knows that you went with her? I honestly can't remember but I just did JKK again this run and I don't recall anything that ruins this theory.
She asks you to go along either because she likes you or perhaps she suspects a trap so she wants the new guy (who she's been real friendly with) there to test the waters for her or help her in case it's an ambush. You fall in the trap instead and she realizes it was meant for her. She sticks around to help you get out, then either lays low (like Bogdan) or flees the city. Ola doesn't know you went with her; you ask him where she is and he says she's gone; he thinks she fell through the trap and is dead or stuck down there. He knows she was real friendly with you and wants to test your reaction. Remember; he's a liar and a bad guy in general; you can't just assume he's telling the truth. If you tell him you don't care and you didn't like her anyway, he's thrown off, but he still doesn't say how she died or what happened to her or even that she is dead.
Or she could just be dead; I don't think there's any actual evidence either way.