Remember airpower also played it's part, land based strikes against outposts and supply lines, or B-29 raids on Japan, they sowed thousands of mines which brought coastal shipping to a halt (It also made 1945 a year of slim pickings for U.S. Subs, as there weren't many targets left!).
Carrier based strikes also hit how as they helped strip away the naval and air protection given to merchant vessals (in whatever form it took), to the point where they were sailing within sight of Japan.
Can't wait for SHIV as it's been years since I played in the pacific (I missed out on the original Silent Hunter)