(SPOILERS) Plates at end

Here we go...

BUMP!!!

I came here to ask exactly the same question. I thought exactly the same way as you when I saw that scene.

Masa asked Nick about the missing plates because, even though Nick had saved his job and his honor, Masa was still suspicious about Nick. Remember earlier in the movie they had the discussion, over noodle soup while tailing Sato's agent (the girl), about Nick stealing money from drug dealers in NYC; Nick admitted it, and Masa was somewhat disapproving.

So at the end, Masa asks Nick about the missing plates because he suspects that Nick might have taken them for his own personal use. Nick's response in the conversation is evasive, that a guy with the plates who knew the right people, could write his own ticket for the rest of his life. This leaves Masa hanging -- which Nick intends to do. He gives Masa the shirt, and walks away.

When Masa opens the box and discovers the plates, he is not intending to use them to better himself. That would really violate the point of the movie, which is that he has been a good example to Nick, and that Nick has redeemed himself by learning the value of being honest. Masa sees the plates, and realizes that Nick has really been transformed. He calls out to Nick to acknowledge this transformation. And that is the real gift that Nick gives Masa.