the only thing my mod does is increase how long it takes for ships to sink, roughly 10x longer than stock. It does not change the hit boxes.
v2 lowered the torp damage by 50% with corresponding reduction in the ship damage, to maximize the chances that the ships will sink from flooding. Make sure both files are installed and have not been overwritten.
Most BBs take 2-4 torps to sink. Yamato generally takes 6+. CAs 2-3, DDs 1-2 which actually fits in to historical accounts.
CVs will sink with as little as 1-2 torps, may be a problem with the stock game, although again this matches most historical accounts.
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