I just got my combo pack in the mail from Amazon... there are indeed 2 discs.
HOWEVER... the case is not designed for 2 discs, either with the extra disc holder slot, or the longer peg that Halo 2 CE or Tom Clancy Trilogy has. Instead, they give you the Sonic Mega Collection Plus disc on the peg, and a paper envelope with Super Monkey Ball Deluxe in it.
What is even more odd is that the Sonic disc is the Platinum Family Hits version... but the Monkey Ball disc is a standard, original disc.