@WatsonWork
I think what @atsond12 meant to say was excused and not exempt. In that case for an assignment where a student is excused, they still show up in the list of students to receive the message from "message students who..."
@atsond12 what you will have to do is use the "message students who..." and then view all the students and remove all the ones that are excused from the assignment.
I checked in my playground and excused students are still used in the list of students to receive that message. To me that sounds like a bug(or an oversight) on Instructures part in the coding. It should be put in as feature request to bring it to their attention (I guess). I do not know the best way to get the attention of someone to fix this issue other than a feature request
If a student is excused from an assignment, then they do not need to receive messages indicating they have not submitted the assignment or they have not scored high enough.