I thought the ending was a little bit of a letdown. I really enjoyed the arc, and loved the take on the Joker, but felt it was all too neatly wrapped up. Something more significant should have happened but all we got was that, maybe, the Bat family doesn't trust Bruce as much. That's not new. While that might have long term effects, it's not really shown in the book.
Don't get me wrong, there were parts of it that I liked. It was an emotional issue at times but I think there ended up being one too many cop outs.
In regards to Joker knowing secret identities, I took it that he doesn't know who any of them really are and doesn't much care. He pieced some things together to fuck with them but more than that he can't be bothered.