If my opponent has Secret Actions in their hand, scrap pile, or even in their KO area (say because of
Daring Escape), do those count?
[Source: WotC] 
No. Decipher counts only the Secret Actions in your opponent’s played area.
If my opponent has one face up Secret Action and two face down Secret Actions, do I do 1 damage to each enemy, or 3?
[Source: Aequitas]
You would do 1 damage to each enemy, then 1 damage again, and then finally 1 damage again. The 'or' in "face up or face down" should be read as 'and/or', and the damage is one at a time rather than all at once.
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