It is possible to use an entityquery which selects different columns from different tables.
The List you'll get is a List of Object, or if you don't want Object, you can specify your own holder object which holds the result, see below:
select new my.package.MyValueHolderObject(col1, col2, e.col3)
from Entity e
left join e.children1 col1
left join e.children2 col2
where e.property = :something
In this case the List will consist of MyValueHolderObjects.
Thanks for your help, Serkan!