If you dont get Kraids last line, the phrase Knock, knock should hopefully make it a little clearer. As for the rest of Kraids lines, I said he was a little slow witted, I never said that he had no booksmarts.
So... Magus wiped Duo out of existance? What a way to go...
He said point of origin. That just means Duo was blown clear.
from what i saw in megaman 8, I think Duo has the ability to convert himself into a kind of non corporal form, which is how he's able to travel between the stars and such. I think in the opening cutscene of the game he was forced into that form when he received massive damage battling the avatar of dark energy in space.