"No, Kichijiro was trying to express something different, something even more sickening. The silence of God. Already twenty years have passed since the persecution broke out; the black soil of Japan has been filled with the lament of so many Christians; the red blood of priests has flowed profusely; the walls of the churches have fallen down; and in the face of this terrible and merciless sacrifice offered up to Him, God has remained silent. This was the problem that lay behind the plaintive question of Kichijiro."
This idea also comes up again when Rodrigues is captured and then interrogated by the samurai. In the case of this novel, I have to go with what I can see from the words on the page. Yes, there is some historical context that is guiding this story, but this world may not be exactly as our own. This Japan is dark without much hope to be had. Rodrigues comes face-to-face with so many conflicts and problems that one begins to wonder if Kichijiro is right in his thinking that maybe God doesn't exist, or remains silent for some nefarious reason. These problems happen, obviously, to move the plot along and keep the story interesting, but I can see where these characters get this question from. God, the one whom all this is for, isn't helping, isn't comforting, isn't saving his servants. This may be why Kichijiro ultimately decides to apostatize and betray Rodrigues.
We can even see this in the greetings of Rodrigues' letters in the novel. In the first few chapters he opens his missives with "Praised be Christ" and "The peace of God. Glory to Christ." But by chapter three those exaltations have been left out. Is it possible that this is because Rodrigues feels the hopelessness of his situation? He subconsciously stops praising Christ and God, because he feels like there is nothing to praise? Possibly.