The (relative) success of Catholic missionaries in Japan during the late 15th century was a temporary and localized phenomenon. Minor lords in Southern Kyushu during the Sengoku Jidai had much to gain from converting because it attracted Portuguese trade, which brought firearms and Chinese goods (which the Japanese at the time were banned from procuring directly.) Once Japan had a domestic firearms production and the Red Seal Ships system was in place, no more lords would convert, which means that Christianity was always bound to at least stagnate in Japan.
Without persecution it could have survived as a local religion in parts of southern Kyushu, as well as a couple of small congregations in major cities like Kyoto and Osaka. Full conversion of Japan is impossible imo. Buddhism and Shinto was organized and ingrained in the country's political and social structures, they would not be easy to displace.