In my experience, no. I recently purchased a 2006 tailgate with hinges from a salvage yard to replace my 2003 TJ tailgate. The tailgate itself fit perfectly, but the newer hinges attached did not.
The problem seems to be where the newer hinge bolts to the rear fender. The newer fender has a recessed area where the hinge attaches. My 2003 fender did not have this.
The good news was that my original (2003) hinges worked perfectly well with the newer 2006 tailgate.
Hope this helps!