I think the secret is more likely to be related to the Lodge and politics, especially considering the rest of the conversation. It looks like CDPR did not have clear plans with Yennefer at the time when TW1 was made, and she does not seem to be mentioned anywhere in the game.
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Yeah i think the secret is related to the lodge's political games and nothing to do with Yen.
Personally i think she reacts very genuinely to the news regarding Yen and i think she would have reacted very differently if she'd been holding this secret since TW1.