Over time I've evolved a combined approach. I originally started with the one big document version, which tended over time to accumulate some clutter due to a large number of agents piling up and so on; this did get inefficient in some ways. Some cleanup was eventually done, mostly by deleting a few dozen agents and bells and whistles and reorganizing. I still use this (>5000 notes) daily for a combination of a journal that goes back a number of years, with accumulated notes on books, movies, articles read and so on; I used to add specific dated notes on random topics of interest into the journal using the daily journal note as a container but now I have a separate section using a chronological approach just listing notes (on ideas, newspaper clippings, etc.) under month/year containers (modeled on something I think I saw Dominique Reynaud using). I also have a few major topic areas that have collections, such as a large number of notes on using Tinderbox itself, general career planning ideas and bucket lists, and so on.
But I also use many dedicated larger and smaller documents. One is a general notebook for my writing avocation, which includes sections on the business aspects of editing and publishing, and a sort of working data bank of ideas and project tracking sections on the creative work. I keep a separate document for matters related to my psych practice for memos, copies of email discussions, information on things like test publishers, brainstorming and decision-making notebooks; also a document on using Tinderbox where I save up tips and how-tos which I am gradually organizing into a personalized "user manual."
Finally, I use a lot of specific project documents for writing or work projects or other things; sometimes you just want to focus your attention on one "mental ecosystem" without distractions. For a current writing project I even have begun two separate documents, one just for writing content in a sort of brain dump way, but the other with preliminary book outlines, notes on book proposal ideas, and "platform building" plans and ideas such as ways to develop classes or research on the topic.
I do like the large, "commonplace book" approach to using a large notebook of journals, thoughts, random reading notes and ideas and aspirations and such. It might not be something I'd probably start now from scratch, but it's more like an old friend, a slightly cluttered bookstore that you've been in so many times you know your way around. I can still find stuff there easily, do ad hoc agents or just searches or tag searches, search for similar notes, look up someone's name etc, when need be. It also has links to my large, pretty well organized DEVONthink database which itself has 17,000 documents stored, going back many years.
But for a new writing or work project, your enemy is head clutter, and you want to do things to stay as focused as you can. For that, a small, recent, clean document is often best.
[Note - one minor edit for clarity 1/6/17]