The origins of "but yeah, duded" are not completely known. It is believed to have started in small circles and gained notoriety through the internet.
Derived from "so yes" and "dude". "So yes" is simply used when people have nothing to say; "duded" is the misspelling of "dude", a reference to the person you are talking to. People who often say "but yeah" avidly misspell words.