I am using the setdest tool in ns-2 to generate a mobility scenario that has 200 users and lasts 1 hour. I used version 2. It took seven to eight hours to generate only800 seconds. Is this normal? I hope some people more experienced with this can give me help.

Check the source code setdest.cc under indep-utils/cmu-scen-gen, you can comment out parts that display routing tables. This will dramatically reduce the time needed to generate the scenario.