As someone once said, if, after nearly 400 years, you only have abou 1% market share, your business development, advertising and marketing plans are somehow in need of a tweaking.
Well, it sounds like there was "illegal restraint of trade" for much of those past 400 years. Hard to "market your brand" under such conditions. However, there has also been adequate time between repressions to make greater inroads. So, who knows why Christianity remains a persistent member of The One Percent Club?? You probably have a much better idea than I do.
Personally, I have heard the 1% figure bandied about, without change, for so many years that I am not sure I believe it anymore. One would expect that figure to fluctuate up and/or down a bit over time. I suspect that there may now be more than 1% of the Japanese population that is Christian, but the secular left-wing news media has no interest in reporting such things (or is too lazy to conduct the research necessary to update their demographic data).
Either way, at this point, the way things are continuing to go downhill here in the West, we are increasingly in need of Missionaries of our own back here (and even more so in Europe)!! So, I am not sure we can spare as many for Japan.