You'd have a point if the stat about Japan was about the conviction rate of people who go before a jury, but unless I'm mistaken, the conviction rate we're talking about is that of people _charged_ overall.
That 60% figure in Canada is precisely referring to people who were charged, and whose charges were later dropped. Over 99.4% of people charged in Japan are eventually convicted.
Consider what it means to be charged. This allows for example the police to gather more information by doing what would otherwise infringe on someone's rights. So when you basically never drop charges, that means that either you infringe on people's privacy before they're charged, or you routinely disregard whatever exculpatory evidence you find. Either way, it's obviously bad.