You have two WHERE
clauses in (the external part of) your second query. That is not valid SQL. If you remove it, it should work as expected:
select * from table_A as a
where not exists (select 1 from table_B as b
where a.id = b.id)
AND
not exists (select 1 from table_C as c -- WHERE removed
where a.id = c.id) ;
Tested in SQL-Fiddle (thnx @Alexander)