Hey kensiko,
I am in Ontario and have likely experienced a similar winter to you. My bike also clicked all winter, but I went out to check on it one day and it was completely dead. No green light, no clicking, no nothing. It should be noted that I store my bike in an unheated garage, so it is regularly below freezing. I called Zero, and they told me to warm the bike up, then try charging it again. I ran a space heater aimed at the battery for about 4 hours, then tried plugging in, and the bike charged up no problem. The battery was completely dead.
I had a similar incident about a week later where the green light turned off. I did the same procedure, and the bike started charging again. This time the battery was at 76%. I talked to Zero again, and it sounds like the battery will drain completely in about 4-5 weeks in subfreezing temperatures. To protect the battery, the bike will not charge if it is below 0 degrees, even when connected to the charger. With this winter I would say there has definitely been 4-5 weeks in a row that haven't even approached 0 degrees, so I consider this very possible.
In the manual it states that "Above this temperature (-35), working as a system with the BMS, the charger will ensure the battery survives winter storage with no permanent damage, even if the temperatures dip well below freezing for weeks at a time." I think that Zero has designed it, with the assumption that there will be at least one day every 4-5 weeks where the temperature will be warm enough to top off the pack. Unfortunately this winter has just been so relentless that we haven't had that luxury, February in particular. As I said, it looks like my bike loses ~25% a week in subfreezing temps.
Thankfully we are into spring now, and it looks like my bike survived the winter (with some monitoring)! Zero also told me that there was a firmware update released in October 2014 that improves the cold weather charging behaviour of the 2013 S, but they didn't specify what exactly is changed. My bike is currently at the dealer so I will be having this new firmware applied.