I continue forming questions until each stack is small enough to list as a brief page of links. A few pages belong on both sides of a yes-no question. For those pages, I just photocopy the page and put it on both stacks. These pages are rare, and duplicating them doesn't seem to have a significant effect on the density or complexity of the site. The VA HyperFAQ looks and feels like a desktop application.
Users click on buttons and they walk down a certain logical path.
The intention of the design was to minimize the cognitive burden on the user. The HyperFAQ, like other FAQs on the web, are frequently used by people for whom the primary navigation system has failed. For those people, you want to minimize the cognitive burden. Structurally, there's no simpler cognitive burden than a yes-no question. What's important to me is that the application is easy to use and is customer-focused.