I'm guessing its some ipc that only adds or removes entries, but when you mouseover it sends a signal to the killed process, realizes its gone, and only then deletes the icon from the systray...
By the way, if the app wouldn't respond in time, what should happen with the icon? What would happen if Explorer removes the icon but the app which still thinks it has - would update it?
What happens if your NotificationAreaAPIv2 is not widely adopted?
What happens with the apps what were never adopted to your v2 API? (You still have the problem anyway).
EDIT: And what happens with the old apps when you deprecate the old API?