I have been at WDW several times during Night of Joy. The parks usually close earlier than usual in September just 'cause it's low season. I want to say MK closes at 7 or 8pm. Fireworks are not anywhere near as often either. Maybe 2-3 times a week. I try to stay at a different resort every year and I've had no problems doing that when I travel in September. I can usually get in anywhere I want - I usually book Apr, May, or Jun.
As far as crowds go, September is really a great time. Crowds are lighter. I haven't noticed any significant difference at MK on the actual dates of NOJ vs other dates before and after. Pretty much the same.
Personally, I don't mind the shorter park hours. I find that if the parks are open later, I stay there and ride things 2 or 3 times. Now that's really great and definately nothing to complain about. But with shorter park hours, I ride everything once (and with the lighter crowds, you can do your favorite attractions alot quicker 'cause the lines aren't long), hit favorites twice, go to the hotel and clean up. Then I like to go see something I haven't seen before. Eat in a new restaurant, visit a new club at Pleasure Island, or enjoy my resort's pool.
I just try to see it as an opportunity instead of a drawback. This will be my 8th time in 8 years and I still haven't see everything yet - not by a long shot. So many restaurants, so little time at WDW.
Now all of this info from past years may be different now because of the Fairytale vacation package. Hotels are full and parks are crowded. Hard to say this year.