"Ca fait combien?" follows the usual pattern when u want to calculate a sum. U may know that "2 + 2 = 4" usually reads in French as "2 plus 2 égalent 4", but kids learn saying "2 et 2 font 4". U can use this expression for anything you can count and add up. E.g.: Ca fait combien de jours que...?.
Now, I rather think that "C'est combien?" is restricted to asking for prices, as a kind of short form of "Ca fait combien?". U can then get the answer: "C'est 3 euros", etc., but other possibilities than counting money just don't occur to me. (U dont have, for instance: *"C'est trois jours.", *"C'est dix personnes.", even with the plural form of the verb..).