。
It seems she knew the secret.
Literal
She [topic-は] that secret [object-を] was-knowing [seems-ようだ].
~ようだ marks an inference based on observation or evidence — 'it seems, it appears.' Slightly more formal and evidential than ~みたい, less hearsay-flavored than ~らしい. Pairs naturally with 知っていた (the past stative of 知る), describing a state of knowing that the speaker is now reconstructing from clues. The whole sentence frames third-person epistemic guesswork: someone has reasoned backward to her knowledge from outward signs.