Interesting; I didn't think to try it without the UNION. I suspected UNION ALL had something to do with triggering the problem, because plain UNION does not show the bad behavior, i.e. this returns both rows:
SELECT *, sqlite_version()
FROM (
SELECT NULL val FROM (SELECT 1)
UNION
SELECT 'missing' FROM (SELECT 1)
)
LEFT JOIN (SELECT 1)
ON val IS NULL;