It's quite prominently displayed in the details pane: http://www.flickr.com/photos/seldo/5021847660/
And even more so on the tweet's individual page: http://www.flickr.com/photos/seldo/5021848326/
It's absolutely still there. It just moved a little bit. Non-story.
The application attribution was always of interest to a minority of users. I think it makes a lot of sense to move it to the details pane, to keep the stream simple and give greater prominence to, e.g., the favorite link, which is much bigger in the new layout.
I think anyone developing heavily for one platform should always keep in mind that you'll need to pivot as quickly as the platform company.
I thought most users view tweets not through the twitter stream on the web but using clients. The clients may or may not show the posting app's attribution, so I don't see this as a major shift of the status quo.
Also the mobile web version doesn't have this attribution either: http://mobile.twitter.com/
There are many reasons to log into twitter.com, and so the graph needs to break out (or at least explicitely state) how many people read tweets on twitter.com.
Another, more important, point: there is probably a long tail effect here. I have a hunch that when you aggregate all reading via API vs reading via the web, the breakdown would show a huge API to web ratio.