2600 pounds of explosive not deadly to shipping? 
Sure it is. But it had to be lugged by a bomber that had become pretty much outdated by 1943, let alone 1944, and during a World War a couple of years is an eternity for design and development.
The Mother bomber did its best work in late '41 and in '42. By the Spring of '45, when Ohka was finally ready, the Betty bomber was a sitting duck to the highly advanced defenses of the USN carrier groups. If they even had a land based strip to take off at in the first place. There were about 800 Ohka's built and to the best of my knowledge they only sunk 2 or 3 small ships, the largest being a USN DD. Well since the Ohka was being launched against a USN that had about 6800 combat ships, including about 161 CVs of all types, 377 DDs, 23 BBs, 72 CAs, 361 frigates, 2600 amphibs....ect I dont think they got very good bang for the buck from their little cherry blossom.
The Betty had to get about 20 miles from the CV just to launch the thing. Then it had to somehow avoid the CVs pickets, defensive fighters, AA guns, to get to line of sight where it could touch off its rockets. Its no surprise the thing was virtually useless in real life, "tho I dont doubt every 15yo in the game would love to get their hands on one". We dont need more ways to sink CVs. We need more ways to protect them from the fun Police.