The recent addition of Clipper card readers at the ferry terminals in Alameda and SF looked like at long last the ferry service was going to get Clipper support so books of paper tickets would no longer be needed. And so it is, on October 1st.
Unfortunately, as with many aspects of the SF Bay area public transit system, those in charge of planning the addition of Clipper apparently don't use the service at all, or even listen to people who do.