The actions of the Joker in TDK will definitely have lasting repercussions in Gotham. He killed all the major crime lords in the city and took over their organization, though with entirely different goals.
It would be impossible not to acknowledge this and have it serve as a jumping off point for the story.
However, I think the Joker should only be mentioned specifically once or twice in passing, a la Carmine Falcone's shout-out in TDK.
Anything else would be distracting.