That's true. In fact, they already are:
http://itunes.apple.com/us/app/super-monkey-ball/id281966695...
Rich apps like Google Wave, however, can be accessed directly in the browser, as can apps like Gmail and Google Latitude. It's unfortunate that the majority of these apps are developed by Google, but frameworks like iUI and jqTouch bring this kind of functionality to the broader web.
I think it's silly to suggest that Apple's app links that redirect to iTunes are somehow equivalent or equally meaningful as fully functioning applications.
By your reasoning, there's no URL for GIMP either. Does that make it part of the URL's death knell? (I wouldn't consider a URL to an Debian repository to be much different than a URL to an App Store, after all...it doesn't take me to the program, but it will allow me to configure a special piece of software to obtain & install the program for me.)
Meanwhile, Flash gets no mention in the article?
As well, to the best of my knowledge, no one besides Adobe can change the underlying Flash spec, so I would completely disagree with your assertion.
Even if I had to pay Adobe to create or publish Flash apps, which is not the case, they wouldn't be able to censor me. Big difference for me.
I think that there is a role for App Stores in the future, but I think that the healthiest future would be comprised of hybrid app stores that give you access to the best web and native apps — without having to distinguish. Thus you could go through the app store if you want the exposure, or you could go directly to the web app's URL if you knew it.
Seems simple enough to me.