I had a few minutes to poke about with a Synergy manual I found online.
It looks like by default blank scores are set to be not scored, and there isn’t a way to change that. However, I found this, which is a way to quickly enter zeros for blank cells in an column:
“Tip: To enter the same grade for all students for the assignment, enter the grade in the first student’s line and then click the green arrow ONCE to copy that score to all students below that line. If a majority of students received the same score except for a few, first enter the scores for the students with different scores, click Save, then from the top of the list enter the score all of the rest of the students earned and click the green arrow. Clicking the green arrow once fills in the rest of the blank cells without overriding the scores that had already been saved. Clicking the green arrow TWICE overrides all previously entered scores.”
Likewise, there might be a way to enter the same comment (missing) for all blank scores in an assignment? I haven’t found that yet, but if so, it’d be a lot less clicking.