i would think that, once upon a time when it first appeared, it was to give the user options, depending on which way the storage media went, in the future, possibly similar to what nikon is doing with the dual (but different) slots in the D4 but thats just a guess...
technically speaking, saving space may have been an issue, but again, its a guess.
practically speaking, NOW i love it, because it gives the option of using an eye-fi card, which i do.
currently i use a canon 1Ds2, but im looking at moving to nikon for the D800. currently i shoot RAW + medium jpeg. the card is set to keep the raw saved, but send the jpeg to my imac or ipad for a quick preview and later i will move the RAW files over and delete the jpegs. its really helpful for me and my seniors as we work together in a session.
if i move to the D800 (and that looks VERY likely) i will shoot both CF and the eye-fi SD at the same time. i believe there is an option to direct which file type goes to which card, so i will have the jpegs go to the eye-fi and have the RAW go to the CF card. the D800 will have some sort of menu options for the use of eye-fi cards, but, honestly, i get along just fine without those options in my canon, so nikon being aware of the product should certainly do anything but hurt its functionality.
now i doubt the eye-fi card is WHY nikon chose CF/SD, since im sure nikon would be thrilled to tell you their wireless transmitter, but i can at least mention one practical benefit of the CF/SD slots if you have a workflow similar to mine.
im sure im in the vast minority on this, but the CF/SD slots in the D800 are actually a small, but not insignificant, check mark in the "move to nikon" column FOR ME