I hope they've recruited the right people who sign off on their security practices and know all the tricks inside out rather than some clueless civil servant.
I know that Japan has one of the most strict screening process out there but thing is their screening process on crypto exchanges are more focused on the liquidity/financial health of the company running the exchanges as well as how these companies will be implementing the KYC/AML procedures they required to them before they get licensed. The FSA's screening process might be pointed more on how a crypto exchange can run fully operational rather than the security of it's platform so maybe that is the reason why hacks are still happening in Japanese crypto exchanges.