Parece que você deseja
GROUP BY name
em vez de GROUP BY name, dep_value
SELECT name,
Rtrim(Xmlagg (Xmlelement (e, dep_value
|| ';')).extract ( '//text()' ), ';'),
Rtrim(Xmlagg (Xmlelement (e, id_dep
|| ';')).extract ( '//text()' ), ';')
FROM (SELECT emp_name,
dep.dep_value,
dep.id_dep
FROM emp
inner join dep
ON emp.name = dep.name
WHERE id_name IN (SELECT name
FROM altname
WHERE id_emp IN (SELECT id_emp
FROM cnames
WHERE emp_lvl LIKE '%GGG%')))
GROUP BY name