I agree that it is pretty typical of the older grades to keep their assignments/homework in order until the end of the quarter/semester, whatever. Not only for organizational skills, but for review purposes as well.
However, to give a test on "What was the answer to HW assignment #35, question #6", is a little over the top, even for the most organized of kids.
I do agree that the process of organizing the assignments is part of the learning process needed for essential organizational skills down the road.
Loreli, if your son has a 504 plan, I would not take on the task of this if it is overwhelming to you and your DS on your own. In his case, if it is something the teacher is requiring, and is something your DS is having a hard time with, then the teacher should be able to have a plan and help him with it. A partnership~
I would definately bring it up at the meeting and see how you can work together on it.