Why did the brothers not reply to Yosef's question?
Oznayim la'Torah: Because, seeing as he wanted to cry - as the next Pasuk testifies, before they had a chance to answer he gave him a short Berachah, in order to make a quick exit, 1 so that they should not see him crying.
Ha'amek Davar: It was a rhetorical question. Is this your small son through which we can resolve the truth?! He is an adult of complete intellect (perhaps you schemed with him to corroborate your false claim)! In any case, I have no claim against you; you did what was incumbent on you.
Oznayim la'Torah: And this also explains why the second "va'Yomar" has a 'Patach' under the Mem, unlike the first, to hint that he rushed (saying so, so he could go to cry).
Why did Yosef bless Binyamin, "Elokim Yochnecha"?
Rashi: To place him on a par with the other brothers, to whom Yaakov had already applied the term 'Chen,' 1 before Binyamin was born.
Seforno: Since he was the only son of his mother, 2 he blessed him that he should find favor in the eyes of his paternal brothers.
Ha'amek Davar: Do not think that I put an Ayin ha'Ra on him, that he is not small (i.e. he should not grow more). Rather, I bless him to grow more and more!
See Bereishis 33:5.
Seforno: See Bereishis 44:20. (It says there that they had told Yosef that only Binyamin was left from his mother.)
Why does it say "Ben Imo"?
Ha'amek Davar: This explains why Yosef wanted to cry.
QUESTIONS ON RASHI
Rashi writes: "May G-d give you grace (Chen), my son! - We find the term Chen used regarding all of the other tribes...." What it is unusual in this blessing, that leads Rashi to explain it?
Gur Aryeh: Usually a blessing contains the word "bless" (e.g. 'May G-d bless you, my son)! This blessing is unusual in that regard, so Rashi tells us why Yosef selected the word Chen (grace) in particular.