。
She noticed that the money was gone.
Literal
She [topic-は] that money [subject-が] is-gone [the fact that-のに] noticed.
The のに here is *not* the 'despite / even though' のに — it's the nominalizer の plus particle に, where の wraps the preceding clause into a noun-like unit ('the fact that the money is gone') and に marks that fact as the trigger of 気がつく. Identical surface, completely different grammar. なくなっている is the resultative form: not 'is in the act of disappearing' but 'is in a state of being gone'. ~に気がつく ('notice X') consistently uses に for what was noticed.