In his commentary on these verses, R' Samson Raphael Hirsch suggests related tentative answers to both of these questions.
First, he suggests that "מטה בני" - "the tribe of the sons of" - connotes "the tribe as the higher unit to which the individual -בני subordinate themselves." Given that, perhaps Yehuda and Binyamin, for whom the בני is missing, are meant to be thought of as more subordinate themselves to the larger whole of the nation than the other tribes are, since their territory was destined to have the national Temple on it.
Related to that, these two tribes, and Shim'on, which lived inside Yehuda's territory, perhaps thought of their own tribal leaders as a little less elevated ("נשיא") than the other tribes did theirs, since they were so close to the geographic focus of God's sovereignty.