So you're invoking popularity, but I don't understand what that has to do with it.

I use web apps all the time, even on mobile. And I'm sure I'm not alone.

Speaking of which Fastmail's Android and iOS apps are just the web app packaged in a native shell ;-) and they are not alone. For them clearly it was cost efective to work on that web app.

As for why they bothered to package their web app in a native shell? Maybe that's were the problem is.