Researchers point out in this Kumanichi article that the creation of Kumamoto Castle in its current form was no easy task, instead being the result of a series of disasters both natural and man-made that extend back to just shortly after the castle’s birth. In particular, damage by earthquakes, heavy rain and typhoons in the early Edo era shaped the walls, moats, and turrets as we now know them.
A list of the more catastrophic natural events is provided at the link (it omits those man-made such as damage inflicted during the Seinan War); events the article singles out are an earthquake and subsequent explosion of a powder magazine in 1625 which burned down the keep, an earthquake occurring during heavy rain that destroyed 36 meters of wall in the Honmaru area in 1633, and an earthquake in 1889 that damaged walls at 29 locations over an area of 2,700 square meters that cost (okay - quick calculation) - a LOT of money to repair. The article notes that historical rulers of the castle learned to anticipate damage and put aside funds to cover maintenance and provide for periodic disasters.
The article concludes by noting that the castle has suffered in the recent quakes damage to 13 buildings of cultural importance and to 53 locations along its walls, but that, as one researcher put it, “Kumamoto Castle is after all but a compendium of repeated disaster and repair.” - William