I only have 1 child. She is currently 12. I've taken her to Japan on vacation 7 times (we don't have family, but we do have friends) She went at ages 5, 6, 7, 8, 9, and 2x at 12.
We had a blast going in December and if we can swing it we would go back in a second. You do have to look out for New Years closing (and if you want to go to a specific shop or niche location, the closing time can be quite long, I'm looking at you Licca Castle) It is cold, but I think being prepared for the cold is easier than being prepared for the heat because it is easier to bundle up, just be aware it can be cold. Japan felt really cold to us in December 2022, but we were also coming from Hawaii which even when it is "cold" is 70+
If you celebrate Christmas, be prepared for it to be celebrated in a very secular way (aka nothing closes on Christmas, so many people on reddit ask about what is closed for Christmas and it's like nothing, except if Christmas falls on a Monday and then things are closed because it is a Monday.) We love it, because we don't celebrate Christmas.
If you want to see thatched roof houses and you can work it in, Takayama 's Hida no Sato is your best bet because they actually offer craft activities and other participatory activities making it more fun for kids. I thought Hida no Sato was more interesting than Shirakawa Go as well, despite going to Shirakawa Go in February and Hida no Sato in June.
I know Shiga Kogen which is above the monkey park opens for skiing in early December most years. If you're interested in skiing or snow play, it's a fun destination.
The ninja museum and ninja village are closed in December, so I am not sure Togakushi would work, unless your kids want to hike in possible snow to see a shrine. I personally think Shiga Kogen is a better bet, since kids are more likely to enjoy snow play. We didn't ski, though it was very popular we mostly did sledding, which was a lot of fun. Since you are two adults, you could split up.
My daughter didn't like Matsumoto Castle, but did enjoy the small city art museum. It's small and not terribly crowded.
We enjoyed Nabana no Sato, 1 hour from Nagoya, a lot in December. I wanted to go to Nagashima Spa Land as well, but it didn't work out. We did strawberry picking, which my daughter really enjoyed.
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