Is there any possibility to show all files of all groups and subgroups of one database, clicking on the root group does only show the files in it, but not of all subgroups. Or is it the best way to do this with a smart folder, showing all files of the database?
No, this is not possible and yes, a smart group is the only way to do this. It could target a database or individually target a group, showing the contents of the subgroups.