Hi I have almost the same situation as you. My parents are not divorced, but he left us 20 years ago. I decided to get an affidavit made where my mom indicates what happened. Affidavit's are legally binding even though there is no legal separation. Also, I have indicated them as legally separated in the forms and have not included him as a dependent. Lastly, we have prepared an explanation letter explaining the situation and my mom makes a solemn declaration at the end that she will never apply for PR for my father at any point in the future.
I did a lot of research in the past few years to understand the meaning behind adding spouse as dependent even if they are not accompanying you. My understanding is that IRCC requires it, and all the background checks and medicals because if they didn't, one of your parent who receive's PR may call their spouse to Canada through spousal sponsorship which does not have such hurdles as parent sponsorship. Basically, a spouse, may slip through the system even if some requirements are not satisfied, for example, they may be a burden on the healthcare system. Therefore, declaring that your parent will never sponsor their spouse should suffice along with affidavit.
