Hi Nick,
please note the difference between products - SKUs and Documents - documents "presentations" of the product. See the note at
http://devnet.kentico.com/docs/ecommerceguide/products.htm and also related articles.
One SKU can be assigned to only one department at the moment (Or I'm missing something there), so I'm not sure if you mean products or documents in your structure.
Could you please clarify this a little? Thanks.
Regarding the nodes (documents) in the content tree, you could use NodeLinkedNodeID (if it's not null or zero) to obtain the original node. See the API reference for details.
Regards,
Zdenek