I don't find your hierarchy needs at all complex - if you do some searching in this group's archives (
http://groups.google.com/d/msg/tiddlywiki/Ov4LjtQVWPw/YcVIb6Wni7sJ) you'll find this is very much a pet topic of mine, but I'm afraid I don't have quick and easy answers for your actual question, but hope you find the below somewhat helpful in a larger context.
I have been doing exactly what you're seeking for many years, but using Evernote rather than TW. As you're discovering, TW does let you set up the facility to tag anyway you like, and easily retrieve based on single tags, but I haven't found any canned solution that gives you good hierarchical summary display and navigation "out of the box". I'm sure it can be done, but I'm sure it would take a competent and TW-familiar javascript programmer a reasonable amount of time to accomplish, and of course different people have different ideas as to how such a scheme should work.
What I do is use Evernote for my "collection and processing" of random snippets from texts and the web, brainstorming notes etc, and evolved over time the content-specific topic tagging index terms hierarchy. Evernote's very very flexible and forgiving of changing meta-organizing schemes as you go along, there really isn't anything stopping you from setting up as many different ways as you like for slicing/dicing the content, the ability to select a sub-branch of your tag hierarchy, then do various AND/OR combinations simply by clicking/shift-ctrl-clicking on the other branches or single tags is really a thing of beauty from a UI ease-of-use POV.
Once a given topic area and it's organizational taxonomy has started to gel in my brain, I then start moving the content over to Tiddlywiki, which truly excels at cross-platform and portable storage and presentation, but I've found you have to have a reasonably well-developed idea of how you want the end-user to navigate through the data, set up a traditional, not-too-deep navigation hierarchy, perhaps coupled with a listing of all content-indexing terms for them to browse, along of course with intra-TW tiddler linking from within the inline content.
I really like "true hierarchical" tag navigation, where you can select a parent tag and all its children get selected/filtered at the same time. That is why I have stuck with Evernote v2.2 over the years, as when they went to their cloud-model newer versions, they implemented a tagging scheme that could be made to look hierarchical but in fact didn't work that way under the covers.
However there's little support and it can be difficult to find, probably will be issues with future OS versions, etc. So I'd advise checking out the current version of Evernote and see if you can make it work for you. If not contact me and I'll set you up with the older version to see if you want to go that route. Or of course feel free to ask specific questions on what I'm doing in TW in this area here.