pragma can respond to normal queries.
Dim response As String = SQL.ExecQuerySingleResult("PRAGMA encoding")
Log(response)
logs "UTF-8" on my system
issue your SQL.ExecNonQuery("PRAGMA auto_vacuum=0") as normal
and then issue SQL.ExecQuerySingleResult("PRAGMA auto_vacuum") to see the result.
(note: some commands may not be legal. eg, auto_vacuum can depend on how sqlite was built. you may not simply be able to turn it on...)
check sqlite documentation regarding valid pragmas and any trickiness that you might expect.