Hakodate: beside the places listed above, is there any places of interest?Hakodate has a hot spring resort, Yunokawa Onsen, in its outskirts. It is not really worth a daytime visit, but it could be a nice place to overnight (instead of central Hakodate) if you are a hot spring fan.
intend to stay 3 nights and could it be too long?
Yes, as mentioned before.
Asahikawa Zoo - heard that the zoo is small, is 1/2 a day enough?
I would call neither small nor large. Not including access, half a day should be enough. But it depends on how long you enjoy observing the animals and watching the shows. If you just walk through, you can see the entire zoo in an hour or two, but if you observe all the animals and see some of the shows, you could spend most of a day.
Ski Resort: Intend to stay in Niseko Hilton Village hotel. We will not be skiing, the children will like to play with the snow and some snow activities. is 2 nights enough or should 1 extend another night?
I think that two nights and one full day are enough, but if you wish to play and relax for another day and increase the chance of having good weather, you could extend. It is very much a personal decision to make.