As usual I'm late to the party but I find uses for both a single large org file as well as multiple small ones.
-For knowledge capture, I prefer the quick action of small files, one file per capture instance. I use a personally written system called 'scraps' (with many similarities to 'denote' or 'howm' etc.) which quickly captures one 'scrap' of information to a single (generally small) file. I recall information later with deadgrep or similar fast tools. -But for my fiction writing, including full length novels, it is always one file per project. I don't want to have to deal with identifying multiple files (like a file per chapter or scene or whatever). Org-mode makes this work easily; my research notes are in the same file. It is all very portable and easy to manage with a dead simple version control system like the venerable RCS. As long as I don't use things like flyspell or live word count, performance is more than fast enough even on old slow computers. Another benefit is easily exporting everything at once (with :export: and :noexport: tagging) to LaTeX or odt. -- Bob Newell Honolulu, Hawai`i - Via GNU-Linux/Emacs/Gnus/BBDB