Query #1 is not the elegant way for doing this… (NOT) IN SELECT is fine for a few entries, but it can’t use indexes (Seq Scan).
Not having EXCEPT, the alternative is to use a JOIN (HASH JOIN):
SELECT sp.id
FROM subsource_position AS sp
LEFT JOIN subsource AS s ON (s.position_id = sp.id)
WHERE
s.position_id IS NULL
EXCEPT appeared in Postgres long time ago… But using MySQL I believe this is still the only way, using indexes, to achieve this.