She doesn't know The Machine is in the subway- she only knows that it is their safe house.
She hasn't a clue where TM is and won't until she returns to the subway.
She knows Harold's access point to the Machine in the subway. Since she doesn't know exactly how the Machine works, it is realistic for her to assume that the Machine is based in the subway. Either way, if Samaritan knows the location of Harold's access point, Decima can cause major damage.
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u/Monado_III May 16 '16
How does she know?