With tags, this is not a headache at all. Say you have just acquired a bunch of documents about climate change, natural disasters and climate change awareness. You just do the simple thing – to assign the three tags to each of the documents – while maintaining a flat system of organization, in the sense that all your tags are at the root level (that is, not nested).
At some point you may find quite a few tags with the name climate change xxxx. Then you can assign the tag climate change to each of these tags, and still maintain a flat system.
This method does not actually resemble how things work in my brain. I tend to think in chaotic, erratic, unorganized ways. That is the reason I seek help from PKM software in the first place. What the aforementioned method brings me is the ability to navigate related topics and documents seamlessly, in the sense that I can repeatedly Reveal Tags without having to build a search/smart group or dig through a tree of folders. I believe this saves me more time and energy than those spent on organizing my tags.