Excellent reply, Sinner. Samurai are very much hyped, because people only remember the best of the samurai, while we know about the average medieval knight.
One thing I wanted to add:
Ok, the hygenie is in favour of the samurai, at least to our modern sensibilities, but it might help the knight. The smell might be so bad that the poor samurai's eyes would water & he wouldn't be able to see too well.
It means that the average European would have a much better immune system than his Japanese opponents. I am not saying that it would have the same effect as on the Indians (who were often depopulated before the colonists entered their territory), but it will have some influence if the samurai aren't able to live up to their hygienic standards (like in a overpopulated army camp). So disease works both ways.