I'm not totally sure about the crowds in September but my guess is that weekends are always more crowded. We go a few times a year, always on a Saturday and one day during the week, and at various times of the year. Our Saturdays are always crowded, probably local residents, but during the week has always seemed less crowded.
Big attractions that you should do first to avoid crowds later in the day:
~ The Studio Tram tour
~ Water World Show
and rides like The Simpsons, The Mummy, and Jurassic Park are always busy. The Simpsons line is extremely slow moving, followed by the Mummy and JP.
The rest of the shows are fine, they move along very nicely and shouldn't be a problem, follow the show guide/times to plan your day, but get the Tram Tour out of the way first. The best car to sit in is anywhere in the 3rd car, followed by the 2nd car but toward the back, and the 4th car but toward the front. And most of the tram attractions take place on the left side, there's some to the right but most of the good stuff is on the left side.
I don't know about Hilton deals, but I just stayed at the Sheraton which is next door. If you can afford to stay at either place I would highly recommend it. Both are within walking distance and are on the Universal site, the immediate area especially across the freeway is very scary and seems very unsafe.
Both are walking distance if you are a healthy walker, we had a temporary wheelchair member in our group and we still walked to the park. There is a shuttle available but we found it was quicker just to walk, and just so you know the hotel shuttle departs from the Sheraton and then goes to pick up Hilton guests, so by the time the shuttle arrives at the Hilton it's just about full with Sheraton guests. Very easy to walk to the park but first ask the staff how to get there, wasn't clear at first but it's extremely easy and close.
Good luck!