Technically, not most, "just" less than a third of the actual warships (not counting unarmed transports, which were utterly MURDERED by subs) were sunk by Allied submarines. Most of those were destroyers, as well, as it was rare and noteworthy for a sub to actually sink a carrier or cruiser, and usually was the result of design flaws when they did happen. Kongou was the only Japanese "battleship" (battlecruiser) to actually go down to a sub. (And the last "battleship" to sink to a submarine, ever, although a couple British battleships were sunk by subs, and a quick look at Wikipedia says the French also lost one...)
More IJN warships were destroyed by aircraft, which they were also fundamentally incapable of stopping, thanks to the failure of their aviation training programs and sheer lack of capacity to match the Allies in aircraft attrition. Virtually all the other fleet carriers (including Zuikaku, and all the carriers at Midway) were sunk by aircraft, as well, but for "LOL, so much for 'armored' carrier" Taihou and "What do you mean duct tape and plywood aren't strong enough to stop flooding?" Shinano...
Subs did sink more than direct surface ship fire, though, and fewer still actually survived the war...
