I'm having trouble to understand why the ni particle is being used here.
That's a part of Yakusoku no Neverland manga, when Emma (one of the main characters) is doubting if Gilda is a spy.
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本当に is equivalent of 'Oh really?'
While 本当 just means truth/real/proper
Therefore に particle adds extra doubt to the sentence
Good explanation from a website:
Hontou Ni: The word Hontou Ni has the same meaning as Hontou. However, there is a stronger emphasis on the NI so it tends to be a stronger version of the word in verbal and written form. Examples of "really" in a Japanese formal conversation is: Hontou ni hajimete desuka? (Is it really your first time?); Hontou ni yoku nite iru! (She’s really like you!); Hontou ni sono saabisu wa tadadesuka? (So is your service really free?).
本当 is a 名詞 (noun) or 形容動詞 (no-adjective).
本当に is a 副詞 (adverb).
So you can say,
= a true story
= is that really the case?
The addition of に is not as an emphasizer. Instead, it's that it might be left off in casual speech.
And that 本当に? by itself can be the equivalent of just asking "really?"
In your particular sentence, 本当にギルダー ... is an example of a clipped sentence.
It would mean is Gilda really [a spy]? (i.e. I can't believe it).
Here 「本当にギルダ...？」 means 「本当にギルダが情報源(か)？」, "Is it really Gilda?" or "Is Gilda really...(the information source)?", rather than "Really, Gilda?" The omitted part is cut off.
本当に functions adverbially and modifies the whole sentence 「ギルダが情報源(か)」. You can't say 「本当ギルダ」 or 「本当ギルダが情報源(か)？」; you need to add に for 本当 to modify 「ギルダが情報源(か)？」
本当 is a noun (名詞) or a na-adjective (形容動詞) and can't modify anything by itself:
ほんとう【本当】［名・形動］ -- デジタル大辞泉
ほんとう【本当】〘名・形動〙 -- 明鏡国語辞典
明鏡国語辞典 also lists 本当に as an adverb (副詞).
本当に can function adverbially, but 本当 can't.
(When you say 「本当？」, you'd translate it as "Really?". But the Japanese word 本当 is actually not an adverb. 「本当？」 literally means "(Is that) real?")