Use a Source Node and pick Entire Library, a Project or a Folder.

Then choose 'Tree Structure' rather than 'All Images'. Aperture Assistant will then look inside the Library, Project or Folder for other containers, then look inside them etc. Use the Depth setting to decide how far down to go down into Aperture's organisational structure.

The sub-containers will automatically be added sub-folders in the destination folder. For example, if you pick a Project which looks like this:

Set the depth to 1 you will get the two Brown Folders and all the images contained within them:

Set the depth to 2 or higher and you will get also get the Albums as Finder folders, each containing their respective images:

Avoid using Tree Structure with the Action Node>Add Finder Sub-folder action as this will add even more sub-folders.