After talking about layers I recently read the OGC WMTS specification. A new concept called themes was introduced there, and that lead to me being able to understand the problem I'm trying to solve here more thoroughly.
Layers in WMTS are no longer hierarchical. All that remains of the old WMS layer trees is a single list of layers. In order to create order in a potentially huge linear list of layers, the theme concept was introduced.
Themes in WMTS can be hierarchical, and each theme can reference any number of layers. Layers can even be referenced multiple times, and you can have multiple top-level themes.
That actually makes a beautiful distinction between structure and data. Speaking in deegree workspace language, it suddenly makes a lot of sense to have not only a bunch of layers configured in one place, but also have a bunch of themes, referencing layers, in another place. A WMS would then only reference themes.
Other ideas include simple layer collections (which aggregate layers similar to current logical layers within other layers).
I still have to figure out a lot of the details, but I can feel that this is going to make things simpler. When configuring a layer you only think about what data it's going to use, and when configuring a theme you only think about the bigger picture (where do my layers belong).
I'm always open for suggestions, so if you have an idea about how to make things good in the end, please speak up.