Let me get straight to the point.
Example: 百鬼
The common pronunciation is Hyakki. However, in some sources it is pronounced as Nakiri. There is a fictional character named Nakiri Kuudou from Senshinkan.
My question is why and how?
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Hyakki is from folklore and Japanese monster tales, that of the parade of a hundred monsters: 百鬼夜行
Nakari is a more normal sounding name. I can’t say how common this one is though, but there are other possible readings here to 百鬼 as a name: おきそ and きなり for example, info taken from Jisho linked above.
In the end, it’s about the nanori-readings here. And those are hard to learn I find. Encountering them is a start, but they’re often hard to memorize.
(there really isn’t a way to guess which reading it is, as far as I know, for names. It’s not a word after all)
Edit: now I figured out I can get Jisho to list the names in this case…
The most important bit here is this:
ひゃっき 【百鬼】
Unclassified name
- Hyakki
Its not really a name someone would be called for real. It’s folklore and fictional, referring to a way to name that parade of demons.
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Spoken Japanese came before writing did, so often you have spoken synonyms using the same kanji.
apparently your example is very specific, but it happens for other words
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Apparently there’s a character named 百鬼（ひゃっき）in the Black Jack manga, but judging from the Wikipedia page the cast is full of odd names and pseudonyms…
(You said most of this, but I wanted to pick it out and stress it.)
I think the thing I would emphasise is that name readings, even real world rather than fictional ones, can be not the same as when the kanji are used in normal words. This means sometimes it is simply impossible to guess the right way to read a name. And then when we get into fiction, especially more fantasy type settings, the author might deliberately pick names that “mean something”, including using unexpected kanji or readings, so you’re more likely to run into “not normal even by the relaxed standards of name readings”.
My advice to beginners is “don’t worry too much about names for now” 
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Yes, this is what I said as well. My comment about fictional and real world games is more like a warning - don’t ever take fictional Japanese names you encounter as necessarily something you’d ever encounter - those kanji are more likely read somehow else.
People tend to be subtle with their names as far as I understand in Japan. So, yeah, diminutive names are preferable, while the kanji might suggest something more.
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This was my head cannon for the @latepatate incident! 
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A few days ago, I watched a video where Mike Rowe interviews the guy who created the Pepper X. Quite an unusual and interesting story. The interview doesn’t even remotely go in the direction you might assume.
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