It is possible to recognize both the D-pad and the push-buttons with Javascript on the DSi browser. So I wouldn't be surprised if the same could be done on the 3DS browser, perhaps along with the analog stick.
But again, I think it would be unwieldy, so focus will likely stay on the touchscreen.
How the control scheme will work relies on how the browser works, how easy it is to code, and how smooth it will be for the user. The browser is mainly touch-operated, and that is closely related to why it is simpler to design. Also, it is difficult to mesh both the elements of touch control and push-button control. For example, the battles use touch control for choosing actions, but if walking around used push-button, there would be issues with the player switching between stylus and button. On another note, yes, all the demos so far have been touchscreen-controlled, so that scheme is pretty much set for the final product.
"Every time i click on comment box, the character in game moves! its a bit annoying"
That can most likely be fixed.
Well consideriong that the games that are out are only demos and no where near what they will look like for the 3ds.
So hitting comment and moving will probably be fixed.
Also, get real, it's for the 3ds, so of course Danny is going to use the touch screen, the D-pad is probably for your menu, or backpack.
Taking into consideration the DSi and 3DS browser interfaces (which are fundamentally alike)--alone, A-key or D-pad input won't work. That's why it might work well for menu control.