Here's the data for Japanese warship production during the war, as well as total merchant tonnage produced each year:
http://www.combinedfleet.com/economic.htm
I'm sure if you emailed that site's creator, he could tell you if he has it broken down by merchant ship type.
EDIT: This site gives you every Japanese vessel sunk by sub during the war, organized by which sub sunk it (according to JANAC):
http://www.valoratsea.com/JANAC.htm