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There are no “Separation of church and state” issues.
The subject was never inserted into the constitution.
The clause in the constitution merely protected the right of the states to make the decisions.
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In this case, the State (Missouri) made a decision: the Missouri State Constitution bars any state aid to religious schools. SCOTUS said that Missouri's Constitution violates the federal First Amendment.
That is in part why I put “separation of church and state” in quotes. It does not come from the Constitution, but from misinterpretation of the Constitution.