My problem with the idea that SPAs, as an idea, are inherently more difficult to develop is that this doesn't translate to desktop/mobile applications, which are, conceptually, very similar in architecture (fat UI client, app server on the back-end). What may be more true is that the way in which we develop SPAs is so flawed that it causes serious issues with quality/development effort. IOW, perhaps the issue is with JS and its limitations with large, complex client applications, not the SPA architecture.

Disclaimer: my company sells a web development product that creates SPAs that work like desktop applications.