If your opponent controls an "Embodiment of Apophis" as a Monster Card, it is not counted as a card in the Spell & Trap Card Zone (even though 1 of those Zones cannot be used). So you could not activate "Straight Flush".
If your opponent controls an "Embodiment of Apophis" as a Monster Card, it is not counted as a card in the Spell & Trap Card Zone (even though 1 of those Zones cannot be used). So you could not activate "Straight Flush".