Most people don't disable JavaScript but beyond that edge case (I consider JS disabled an edge case) I agree that this architecture isn't necessary and overused. A single page app is great on a MacBook Pro with 2 tabs open but run that on most "normal" people's machines and it gets laggy quick.
People always mention disabled JS and SEO as pitfalls but I think performance and practicality are the obvious reasons not to do this that get overlooked. SPA architecture is something I use alongside server rendered pages. When you have one page or a series of pages in a particular user flow that would benefit from no page reloads and are heavy on interactivity then it makes sense but otherwise I can't see the value. I think developers will realize this and take a more balanced approached with a practical mix of pages rendered server side and pages that use XHR and JavaScript to enhance the experience.