I think that it is necessary an experiment to settle this… 😉
I’ve chosen a random sim waiting at a station. From his info window, I’ve located the destination. Once it was on the vehicle, I’ve hit the pause button. I have then blown up the destination building and, alas!, a passenger just disappeared from the vehicle…
It seems that Pasi is right, they disappear when the destination disappears.
The only question left is if they also disappear when a time limit is reached, but that is more difficult to check, I’m afraid…