“As for Dad, he is a good one.”
This is a basic noun is noun sentence. The subject is unstated, but based on the context we can infer that the subject is Yotsuba’s father. A noun is noun sentence is essentially saying that the subject noun can be categorized as the noun with だ attached. Yotsuba’s father can be categorized as いいもの, a one good one. Yotsuba’s father is a good one.
In English, this is like saying “A kitten is a cat.” The subject, “kitten”, is in the category of “cat”. The “kitten” is a “cat”.
Now, what happens if we take this sentence, “A kitten is a cat”, and make it the second noun of a “noun is noun” sentence?
We would get:
“It is (a kitten is a cat).”
That’s not really proper grammar for English, so let’s add a word:
“It is that (a kitten is a cat).”
This may sound like an explanation.
“Why are you giving a fresh fish to your pet kitten?” “It is that a kitten is a cat. (And cats like fish, so my kitten will surely like fish as well.)”
Note that in this “noun is (sentence as a noun)” sentence, the first noun (“it”) refers to the situation being asked about.
Going back to the sentence from Yotsuba:
“As for Dad, it is that he is a good one.”
Again, this may sound like an explanation. What is this “it”? It’s the question of whether Yotsuba has an air conditioner at her house.
“Do you not have an air conditioner?” “No, because it is that Dad is a good one.”
It takes a little time to get used to it. (And I might not be the best at explaining it.)