The reason he had no guile is that, although he was wise, he was not embarrassed to follow a simple person. Thus Nathanael expressed in words what he believed in his heart, for he was not coming to Jesus with a desire to tempt him, but out of a desire to make progress in virtue. Proverbs 12:20 complains about a different sort of person: "Guile and deceit are in the hearts of those who think evil things." However, Nathanael does not believe Jesus' commendation until he has some certitude about what he's hearing, because men and women should not be eager to believe the good things that are said about them.
[St. Bonaventure, Commentary on the Gospel of John, Karris, tr. Franciscan Institute Publications (Saint Bonaventure, NY: 2007) p. 130.]