Most simply, because they aren't addressing existence of things other than god in their formulation. They're making a statement about God's own existence. Spinoza is talking about (the connection between God and) the world.
And so does Aquinas: "Article 1. Whether God is in all things? […] Article 2. Whether God is everywhere? […]"
2. According to Aquinas (as you linked), God is "present" inasmuch that God acts on all things ("God is in all things; not, indeed, as part of their essence, nor as an accident, but as an agent is present to that upon which it works"), and Spinoza was certainly more extreme than that. Spinoza thought the world (and everything in it) is a "mode" of God.