Skype's issue was getting the P2P network back up and running ASAP because 1) people pay them for a service that was down and 2) (voice|video|text) chat generally has a higher priority than file sharing. People wouldn't be as ticked off if the P2P filesharing network went down for a few days (or a week) before rebuilding itself.
What happens when all superpeers go offline at once is that the 'normal' peers then start DDOS'ing any remaining superpeers (or the few superpeers that are able to get back up and running quickly). As people settled down with trying to reconnect to the superpeers, eventually the network would rebuilt itself (possibly with completely different superpeers). Once you knock out all superpeers at once, the network becomes quite a bit less distributed.
That said, once all superpeers are down, it could be easy to continue manually DDOS superpeers as their appeared on the network for a targeted attack. If someone was being malicious, they could keep up the DDOS even as regular users are letting up on their inadvertent DDOS due to the sudden change in network makeup.