I think it did.
While TDKR did make a lot of money and managed to beat TDK's box office numbers worldwide...$1,084,439,099 really isn't great compared to what The Avengers, Harry Potter, and Iron Man have done at the box-office in the last few years.
Its obvious the Aurora shooting had a huge effect on the box office numbers, so not many people went to go see it on the first weekend. This ended up effect the publicity for TDKR and the overall box-office of the film.
It also was wasn't released in 3D, which would have help TDKR bring in much bigger numbers than it did.
I just think if it hadn't been for the shooting, it performed MUCH BETTER considering it was the finale to Nolan's Batman and was really hyped and anticipated months before the release.