if cordova polyfilled standard apis for everything it wouldn't be cordovas problem. but right now there are only-in-cordova APIs that I need to use if i'm in cordova. it would be more convenient for me as an app developer if there was a supported way to know i'm in cordova.
I can keep looking at window.location.href and make sure to always run a local web server for development (and never open the file directly on my dev machine) but the point here is that doing those things is more pitfall prone and less user friendly for new devs than doing "if (navigator.inCordova)". if its a ton of work to implement then I can understand not doing it (I dont know what it would take to implement). i'm just trying to say it would be a nicer api :) it seems from my perspective that it would be easy for cordova to tell the browser that cordova is present and it would save app developers from having to use yet another hacky technique.