No they are still running almost every day (there is the occasional day they don't) but I must add the ferry to CA from STJ has been selling out - I arrived in time for the 11:15am and at 11:05 the ferry was full (and loaded) and there were still probably 15 of us in line - they held the 11am Red Hook for us which was nice although not all of the passengers on the Red Hook were not happy that we didn't leave until 11:15 or so. I don't think it has been a problem from CA.
Re. ferries selling out... A few weeks ago when we were on the (10:45?) Cruz Bay>CA ferry, it was a much smaller boat than they used to use. It wasn't sold out, but there couldn't have been many seats left to sell..