Yup, 6-3 is EECS with a CS focus (you still learn basic EE) and 18-C is math with a CS focus. And you're right, MIT does not have an honor roll, though the professors of certain computer science classes have awarded letters of distinction for outstanding performance during a particular class. This is by no means a standard thing.
MIT has never given an honorary degree. This tradition is so deeply rooted in the Institute's culture that I would bet a year's salary that it won't ever happen.
MIT has allowed certain people to serve as "honorary lecturers." That's what Winston Churchill did.
I believe the song said "honor roll", not "honorary". MIT does not have an honor roll.
IIRC it has given out one honorary degree, to Winston Churchill.