How long do we need at Shibu Onsen

In January we will be staying 2 nights in Shibu Onsen. We may not be arriving until the afternoon so will have the late afternoon, one full day and the following morning, before traveling back to Tokyo to experience the snow monkeys and the 9 onsens will this be enough time.?

Yes, a full day is ample of time in my opinion. You don't plan on entering all nine baths, do you? So much bathing can be quite tough on your body.

Yes, I think so. I am a slow traveler but went there for only 1 night from Tokyo and it was fine.
For the snow monkeys including getting there you need about half a day, unless obviously if you stay there for hours on end.
The onsen in the city you can enjoy a few of them on your first evening and more on your second day. Note that on your departure day in principle you can no longer visit them, as you are no longer a staying guest.
The onsen themselves are not huge and indoors only. Some of them can be boiling hot.

You can also visit the village but it�fs very small but nice.

I remember that I had on the Main Street in a typical small izakaya a very delicious dish of karaage.

On the day returning to Tokyo you could consider stopping in Obuse if you are interested.

Enjoy your trip to Shibu Onsen!