That is one of the interesting and confusing (and frustrating) things about doing research on the history of that time. As you said, the Hunley, the David(s), the Midge, etc., whether they were submersible or semi-submersible, were termed "torpedo boats". I believe even skiffs rigged with a spar torpedo were called the same.

Carter refers to the CSS Missouri, which we usually term an "ironclad", as a "Str.", or steamer. In regular correspondence of the time, that is the normal title for a standard steamboat. Just trying to understand what these people were even refering to is an undertaking in itself.