These two phrases are different: ではない, ではないのか.
The former phrase ではない means to negate or deny something. The phrase is a direct expression. See the following example.
Not like; Dislike
The latter phrase ではないのか, usually in the form of ではないか, changes the direct expression to an indirect expression that hints a suggestion or possible outcome. See adapted examples.
Does [one] not like?
Don't children like books?
As a result, the last sentence is now open to more than one possibility of answer: the children like books, the children dislike books, the children neither like nor dislike books. The direct expression earlier is now being questioned and the answer could be any one of those.
What phrase after that
Japanese sentences could omit spacing between words and phrases, which makes a sentence difficult to be identified by parts. Consider the quoted part of sentence from above question.
What comes after 「○○ではないのか」 is a comma and 「など」 that means "et cetera". So the word など is related to the preceding phrase and not related to phrases after that. One could have noticed this, if 「など○○」 had spacing in between.
In Japanese, the word 「など」 is often found in middle of a sentence, and seldom found at the end of a sentence. The trend is opposite in English, in which the word "et cetera" is often found at the end of sentences.
What seiyuu says and why
Now returning to the quoted sentence from the seiyuu, followed by the translation in English. Except for the word ユリゴコロ, this would be explained afterwards.
The story was certainly new (unknown) however, there have had parts that [one] can feel sympathy [in which] perhaps ユリゴコロ does exist (dormant) in the heart of anyone, et cetera.
The seiyuu expressed her opinion by using the phrase 「ではないのか」 to suggest a possibility that ユリゴコロ does exist. But this phrase by itself does not necessarily mean ユリゴコロ actually exist; The fact something that was certain before is now made questionable.
What is ユリゴコロ
The word 「ユリゴコロ」 is invalid (not found in dictionary) and has no definite meaning. Also, the translated title "Nan-Core" does not make sense and has no definite meaning either. Those who actually read and review the book may figure out the intended meaning.
There is an opinion that suggest 「ユリゴコロ」 is a wordplay for 「拠り所」, which literally means "place to depend on". The interpretation may differ, as noted by a thread on Yahoo!知恵袋.
Q: [...] 拠り所をユリゴコロと聞き違えていますが、それがイコールではないですよね？
A: 「拠り所の聞き違え」という一応の説明がありますが、質問者さんのおっしゃるとおりで、この物語に触れた人によっていくつも解釈ができるようになっていると感じました。なので、質問者さんが殺人衝動だと感じたなら、それもアリなのではないでしょうか。正解がないですもんね。 [...]
In short, ユリゴコロ is not equal to 拠り所; There is no correct interpretation to this. That being said, 「○○ではないのか」 is expressing an opinion about ユリゴコロ and the seiyuu may have other related opinions as indicated by 「など」.
- では無い on Jisho.org
- では無いか on Jisho.org
- など #sentences on Jisho.org
- など。 #sentences on Jisho.org (Note the period)
- ユリゴコロ by Mahokaru Numata on Goodreads.com
- Nan-Core by Mahokaru Numata on Goodreads.com
- 沼田まほからさんの「ユリゴコロ」を読まれた方に... on Yahoo!知恵袋