Second, the hashtags (as well as the @replies) both grew organically out of the userbase. They adopted them because the users had already adopted the hashtags. In fact, if I remember correctly, they were initially resistant to the idea until they saw how much people took to them and used them even without any official support.
The new tab seems like a glorified search - they use a hashtag for an icon, but it seems like the system itself would work pretty well for any single-word search. And with a data firehose as fast as Twitter's, you don't really want to have to do search over multiple words if you can avoid it.
Us nerds, we won't care one way or the other anyway.
Just as useful, but can be styled separately. Evolved hashtags, backwards compatible.
Hence, might as well make it a user-manageable item in the tweet itself.
And for my money, the reason they wrap every link through t.co is because this way they have analytics on every link clicked on Twitter. That sounds pretty valuable to me.