So glad that Apple is finally at least trying to make some smart decisions around this. I can't tell you how many times I've gone to troubleshoot something on a friend's computer and they have about 20 apps "open" and no windows. Of course, when I ask why they have so many apps open, they have no idea what I'm talking about.
Since most apps don't implement "close when the last window closes" Apple is simply trying to do some smart checking for the sake of these users.
Except that this problem only existed on OS X to begin with - Linux and Windows never seemed to have it. Seems they manage to ensure that closing the last Window closes an app. The Lion way seems worse than the non-Apple way to me.
If the argument is really "today's computers have enough resources", then apps should maybe never close, not do a Heisenclose in the background.
Since most apps don't implement "close when the last window closes" Apple is simply trying to do some smart checking for the sake of these users.