Just thought I'd post a report on my experience...
Took the Clipper on Jun 27th: very windy afternoon with high seas in Juan de Fuca Strait, so we did a 4.5 hr ride up through the San Juans to avoid the weather. (The normal ride is 2.5 hrs!)
People still got sick. The boat was only half-full, which was nice.
The next evening I took the Clipper back and there was just a gentle swell, so we did the 2.5 hr route across Juan de Fuca and Puget sound. Every seat sold, but it was fine. (I spent over half the trip on deck.)
All in all, a reliable fun way to get to Victoria from Seattle. ^