Can anyone explain the themes of The Samurai by Shusaku Endo?
I have not read this book in 20 years, but since you've asked twice, I'll give it a shot.
To me, the major theme of the book is the twin struggles of Hasekura and Velasco to deal with their human frailties and their worldly problems. The two men have very different situations, but they are both trying to deal with those situations and they both end up (more or less) turning to Christ as a solution.
Hasekura's problem is that he feels isolated. He is a relative nobody even in Japan. When made to go to New Spain, he is even more isolated by being out of place. He turns to Christ as a way of lessening this isolation.
Velasco's problem is more one of arrogance. His arrogance and ambition have been his major troubles in life. He eventually turns to Christ to find humility.
This feels like too pat of a summary because both men's ideas about Christ are not like what we Americans tend to have. So their "conversions" are bit different than we might expect. But I hope this basic idea helps you see what is going on.