Good question. My ex is also on SSI disability. My daughter is 9, so I haven't had to do a FAFSA for her yet. I've done FAFSAs for myself, but not for a child.
The intent of the FAFSA is to determine what the parent's portion of college expenses should be based on their ability to pay. Is it an option to use you and your ex's income for the application? Because his father is on permanent disability, your son may qualify for more financial aid, or grants, than with your husband's income included.
Won't SSI/child support end when your son turns 18?
You may want to call the financial aid office of your high school or local college with these questions. In fact, I might call more than once, to see if the advice you get is consistent.