I find this discussion interesting because I'm not sure what I think about it all. As a [K]Ubuntu desktop user I admit to be completely comfortable with the fixed, nightly update cycle. It's a given -- one of Jeff's assumptions. On the other hand, since Ubuntu works this way out of the box, it's most likely a Windows-think assumption that makes anyone question it.
If absolutely for no other reason, it makes sense to me for open source projects to try to manage bandwidth by staggering updates in a global fashion. That said, unlike eBox, Ubuntu desktop can fetch the package list from the GUI. Since it's not uncommon for a desktop to be shut down at night or, perhaps just as likely, dual booted into another OS, it perhaps makes more sense to have a GUI-accessible update feature than for a server product.
For what it's worth, my own greatest concern is eBox's automatic system update feature. There's no indication, as far as I'm aware, of just what might have been updated, and when. The DansGuardian update from the Ubuntu repos brought down two of my eBoxes, for example. Since I wasn't using the automatic update system, I don't know if eBox would have let me know on the home page that an update error had occurred or not. I might have woke up to two broken networks and had little to no knowledge of what had happened. There is the event system, but I just don't know ... At least with manual updates, I was on hand to witness the issue and so on hand to do whatever I needed (including taking the eBox off line, if necessary) to address any network failures. I'm not even on site every day, and I can't afford the risk of an automatic update breaking things.
For what it's worth ...