Hi Ben,
The ShellObjectItemAdapter.ChildrenQueryModeDefault property is set to TreeItemChildrenQueryMode.OnExpansion by default, which means it only populates children at all when you expand the node. You could change that to OnDisplay instead to populate Children sooner.
The "items" of a ShellTreeListBox control are ShellObjectViewModel objects, which effectively wrap IShellObjects.
Since CanIncludeFiles is false, it should have ShellObjectViewModel.Children.Count > 0 for any displayed folders that contain other folders. But still will not tell you if files are present since those are filtered out from ShellObjectViewModel.Children by the CanIncludeFiles option.
The ShellObjectViewModel.Model returns the core IShellObject being examined though. That has its own Children collection that should have the unfiltered results. Perhaps you can examine that and see if any files are present.