Would like to add to this question.
Not including grades in the aggregation does not solve the problem because then students can neglect to do the work and it won't be counted in the grade. This is a very serious problem that has existed in every version of Moodle--a very good application I have no idea why this isn't being addressed.
Rick's solution looks like it works...I see a lot of issues in the database and program logic that are in the way. Something needs to be done. A fix I can think of is an event an instructor can trigger that updates the gradebook with 0s for all students who have not submitted an activity and already received a grade. It would call the same method we use in the manual grading where we add the 0s...only once for each student that has an empty grade in that assignment.
I won't go on with all the details...but this looks to me like a solution that might work with the program flow and different modules that are involved.
Does anyone have any solutions to this glaring issue? I understand this application was developed for university level applications but would work very nicely in a secondary setting were it not for this major flaw. I don't think the developers really understand the mentality of younger students and what impact this has on a course.