Since 来ない is the negative, I’d guess that it’s because the state of the bus is uncertain. So in this context it’s presupposed that the bus isn’t coming, but they’re wondering if it will?
Well, there’s the negation that @Joeni mentioned 来ない that gives it that double negation feeling to it.
実験がうまくいかないかな with this you again end up with a double negation. I wonder if the experiment won’t go well?
I guess there are more natural sounding ways of expressing it in English (it feels convoluted), but is sounds natural in Japanese.
Edit: I always think of “ka na” and “ka” as something you just attach at the end of the sentence. You first make a sentence, and then decide if you wanna turn it into a question by ending it with “ka” or “ka na”. It’s like an afterthought.
So can it be said that when the person is double negating in this situation, he knows that there’s a high possibility that the Bus won’t come early, but still he is wondering that for a change or once, it will come quickly?
I think in Swedish, it’s be a bit accusatory, like “Jag undrar om bussen har tänkt att dyka upp någon gång?” (as if the buss was sentinent and was deliberately being annoying by not arriving immediately)
Interestingly, you can say almost precisely that in Swedish:
“Jag undrar om inte bussen kommer snart.”
There are some similar patterns in English, too:
“Won’t the bus come soon?”
“The bus wouldn’t happen to be coming soon?”
“I don’t suppose the bus is coming soon?”
While Japanese and English are so distinct from each other that there probably isn’t much of a connection, but using negative forms to soften expressions or express wonder appears to occur in quite a lot of languages, n’est-ce pas?
Edit: I swear this post was somewhat original when I started writing it, but writing at work makes me go at about one sentence per hours
I think the nuance is this: ‘Won’t the bus come soon, I wonder?’, which is how I would translate バスが早く来ないかな, has the implication that the speaker is hoping for/expecting the positive outcome. That aside, I think everyone else has explained the other aspects of this structure, so I believe my work here is done.