I don’t know anything about ACE or the other things you mention, but I implemented Johnny Decimal and leverage Obsidian (all in a single vault). For me, the J.D system helps to implement a top-down structure that marries nicely with the bottoms-up network of my ZK in Obsidian. I use a mental model of a library where the “card catalog” is the Index in J.D. There is a folder just dedicated to the catalog in the same vault and I have “cards” which correspond to each J.D ID, Category, and Area. I use the Dataview plugin to help create dynamic tables of all linked notes that tie to the top-down structure and of course I still have the links between notes themselves, though you’d have to navigate across them per usual. This allows me to quickly add a new note and link it to the appropriate card, then the card is dynamically updated showing not only whatever notes I happen to make about the category, but also a nice table of all the notes that link to it along with some properties/metadata of interest. I made a thread on this when I first implemented it here: J.D Organized and Launched!
I still use it and am very happy with it.