Jesus lamented the hypocrisy of Jews and Jewish leaders. His assessment of Jews (in general) was:
"This people doth draw nigh to Me with their mouth, and with the lips
it doth honour Me, but their heart is far off from Me" (Mt. 15:8. Also
Isa. 29:13; Ezk. 33:31).
Jews, His own people, rejected Jesus, the Messiah who came according to Law and Prophets. Nathanael was not like them. He, according to Jesus' word, the pure in heart (Mt.5:8).
Now, instead, I would like to share the following commentary of Lenski on John 1:47:
"This word of Jesus concerning Nathanael can be understood only in connection with the conversation of Philip with Nathanael. In his divine way, Jesus knew what the two had said and how Nathanael, instead of stiffening himself in his doubt about Nazareth, yielded to his desire for the Messiah and came along with Philip. It cost Nathanael some effort to come to a man from Nazareth; Jesus knows what it cost him, and this rejoices his heart. Thus, we can not reduce this word of Jesus to mean merely that Jesus sees the character of the man Nathanael; we must elevate it to mean the character and quality of his being an Israelite, a man who is absolutely sincere about Israel's hope and salvation, so sincere that he does not allow the mention of Nazareth to turn him away from Jesus. Jesus' word does not mean that in some way Nathanael will prove himself an Israelite, indeed, as Simon would eventually be a Rock, but that right here and now Nathanael is truly what he is.
The relative clause, "in whom is no guile," elucidates the adverb ἀληθῶς, and δόλος is cunning or deception, as when one uses bait to catch fish or some cunning means to secure personal advantage. Nathanael was without duplicity, altogether sincere. David calls such a man blessed, Ps. 32:1, 2. Most men lack this complete sincerity. Professing love to Christ, they still secrectly love the world and the flesh; promising faithfulness, the promise does not fully bind their hearts. This δόλος kept the Jewish nation from Christ, proved the curse of Judas, almost wrecked Peter. Church men and entire church bodies, while making loud profession sonoro tono, yet squint secretly at popular opinion, human authorities, supposed advantages, and with fair sounding excuses deviate from the Word. "Blessed are the pure in heart, for they shall see God," - (Lenski New Testament Commentary - Lenski New Testament Commentary – The Interpretation of St. John's Gospel.)