It's not silly when you consider what longnow stands for. They look at "now" on a 20,000 year scale so the extra zero is just emphasizing that 01931 is still the "long now".
Our written history already goes back over 6,000 years. We can actually understand what people back then wrote. We don’t need unbroken year numbering, or leading zeros, to understand that. The calendar has been reset and changed multiple times. It seems like a mis-focus on something that doesn’t really matter.