I’ll try to explain, but this is one of my least favourite areas of Japanese, so if anybody else can confirm or debunk my explanation that would be great 
The tl;dr is that んですか is short for のですか, and adds a questioning tone to the sentence. You have to add a な in there to make the modification of ん / の by 金魚 (a noun) grammatically correct.
this got long - page 17 question
の can be used at the end of a sentence to add an explanatory tone, or a questioning tone if it’s a question. So のです would be used at the end of an expanatory sentence, and のですか would be used at the end of a sentence seeking an explanation (of course tone can also be used to convey this without か).
ん is just short for の - so instead you can have んです or んですか.
This の (ん) is the nominaliser - in this case it is acting as a generic noun. Effectively you are putting forward this hypothetical の (that you describe) as a possible explanation. This means that you have to inflect whatever comes before properly as you would if it were any other noun. If you want to describe の with a noun (金魚) you have to use な*.
He’s asking whether it - the thing that was stolen - is a rare goldfish (because he’s seeking to understand why it was stolen), so what he wants to know is whether ‘it’ is a めずらしい金魚.
Thus we end up with めずらしい金魚・な・の・ですか, which is shortened here to 金魚なんですか.
[rare goldfish] な [thing] [is it?]
You could indeed introduce the topic as the goldfish, and then ask whether it is rare. めずらしい is an い-adjective, so it can be used directly in front of nouns. Thus a straight question would be 金魚は、めずらしいですか as you suggested, but adding in that questioning tone gives you 金魚は、めずらしいのですか.
Here the topic is ‘the thing that was stolen’ and he asks whether it was ‘a rare goldfish’. It’s just a different way of phrasing the sentence / adds a slightly different nuance.
*I think this explanation is long-winded enough without getting into why?
I’ll leave your other question to somebody else
they’re good questions.
That’s awesome to hear 
SO TRUE. They seem (so far) to be much more important to the story.
That’s absolutely fine - I’m not trying to shame the lurkers, haha, just provide an opportunity to join in the conversation 
Thank you so much for doing so! I’m not sure I really knew that specifically. It’s one of those sentences where I get the gist so just gloss over it, which is exactly what I need to not do 
Yep, I agree with DollyDaydream - どういう means “what kind of”, and かというと is that grammar point we discussed last week which means “if I had to say”.