El problema es que store con id 1 tiene dos registros correspondientes en store_sub tabla, lo que significa que qty El campo aparecerá dos veces para la tienda 1. Debe sumar las 2 tablas por separado en subconsultas y unir las versiones sumadas:
select t1.department, t1.sqty, t2.ssubqty
from
(select department, sum(qty) as sqty from store group by department) t1
left join
(select s2.department, s1.sum(sub_qty) as ssubqty
from store_sub s1
inner join store s2 on s1.parent_id=s2.id
group by s2.department) t2 on t1.department=t2.department
