Sure, we're not going to see native interfaces become part of the HTML5 standard. But it's also not something we should expect. The W3C is big into separation of concerns, which is why we have HTML, CSS, and JavaScript for controlling structure, presentation, and behavior, respectively. If you want to run native code on the client, there are things out there like Google's NaCl (
http://code.google.com/p/nativeclient/) are making it possible.
Secondly, on Android, for instance, you can create an app almost entirely in HTML5/CSS/JS, and execute "native" (Java) code from within the app via a JavaScriptInterface(). In addition (though I haven't used it yet), IIRC you can grant add'l permissions/allow local execution for apps in the Chrome Web Store. So I really don't think it's that big of a deal.
Native interfaces have no place in the HTML5 standard, but most good APIs for building HTML5 apps are going to have an implementation method for that sort of functionality. Already HTML5 gives us local storage w/ SQLite, etc. So for me, it's a non-issue. YMMV.
