We did the Port Hardy - Prince Rupert route in 2007. It was a beautiful day in May and the water was very calm. As noted, there are two areas where you go through open water and we did notice a difference. There was more of a roll, but, as far as I could tell, no one seemed to have been bothered or made ill by it. They also announce when this is going to happen so we were prepared.
We spent the extra money to reserve a stateroom. At that time, it was about $90 and we were glad we did. You have to be at the ferry so early (5:30 AM - very early for us) that it was nice to find the stateroom and go back to sleep for a couple of hours once the ferry had left. Also, it meant that, periodically, we had a place to go to read, rest or just chat, that was a bit more private during the day. Perhaps this would be an option for your mother. (A stateroom has two beds separated by a night table, a washroom with a toilet and sink - and the ability to convert the entire room into a shower room, I think, but cannot quite recall - and a port hole.) I have a vague recollection that they reopened the car deck periodically (to allow people to tend to their pets) for a limited period of time, but I could be wrong and it would be best to check with BC Ferries about it.
It was a very long day. The ferry was to dock about 10:30 PM; however, there were problems at the Prince Rupert end (cannot recall why) and it was nearly 1:00 AM.
I hope this helps. I would think that, over the summer, and perhaps early September, the sailing would be relatively smooth for the most part. After mid-September, the weather is a bit unpredictable. The scenery is gorgeous, although it does not have the spectacular glaciers that you see in the brochures for the Alaska cruises.