Nested queries aren't supported by default, as it is a tricky thing to do.
For now, you should be able to do this:
CoffeeScript:
docpad.getCollection("documents").findAll({
"owner": ({id}) -> id is "12345"
})
JavaScript:
docpad.getCollection("documents").findAll({
"owner": function(model){ return model.id === "12345" }
})