We are using HedgeDoc extensively, from notes in several workshops in our local hackerspace to undergrad/post-grad classes at the university, to meeting notes and it has been a joy since we start to use it, we have accumulated hundreds of notes, and we are dealing with that in several ways, while also waiting that 2.0 allow some plugins mechanism.
Meanwhile, we use tags extensively and some kind of “namespace trick” learnt from Dokuwiki. So, if a page belongs to the something namespace/topic we create something that we call a subpage with an address like something:page. Also, we are testing integrations with mdBook, so pages are created in HedgeDoc are imported into a mdBook folder, which give us detailed search, beyond tags and titles and we may point to the source code inside our Fossil SCM repository or in HedgeDocs (also, we hope that 2.0 allow us to sync variants of the same document stored in several places: HedgeDoc itself, Fossil repositories and so on, with granular diffs being shared between versions).
Hope this helps,
Offray