The HM2 $EV for SnGs factors in ICM as far as I'm aware. So if there's an all-in near the bubble, even if you aren't involved in the hand, it will effect your $EV. Say there are 3 people left in a 6max game, and the other 2 players go all-in, you are rooting for the short-stack to lose so that you can get in the money. The $EV will be adjusted based on the $ you expect to gain in terms of ICM based on how often the short-stack is supposed to bust in that situation.
I'm not exactly sure of all the details of how its calculated, but I know they factor in situations like those.