Such systems are common to MMORPGs, and you know it. All this would do would make transactions needlessly complicated. If you had an item worth one unit and in item worth 100 units why not just use the same unit instead of saying that the one unit item is worth a silver piece and the 100 unit item is worth a gold piece. What would it do except needlessly complicate the money system.
I wouldn't know it, seeing as I play approximately zero MMO's ever. If they do the same, however, it's probably because a game with thousands of players buying and selling things between NPC's and each other would probably need a better money system.
If the computer handles it, and I don't see why it wouldn't, it adds virtually no complication at all. Large amounts of lesser coins are automatically "assembled" into better ones and buying a cheaper item with one will break it up into change of smaller coins. Aside from matters of realism and plausibility, the reason this is better instead of "exactly the same with more colors" is that it allows easier handling of minute and huge values. If all you have is, say, the standard Septim, then nothing can possibly be cheaper than one Septim. It would be such a small amount of money as to count for almost nothing. Subsequently, it would be rather silly for anything to be that cheap; even a simple apple would be way more than one coin, and any poor person will tell you that food is not the cheapest possible purchase in the world. An apple might be 20, but by comparison, a magic sword would be 30,000 or something, and before long you're escalating into absurd money values where apparently you're hiring a gang of teamsters to haul your giant sacks of gold to the store so you can buy something. Smaller numbers of coins makes it easier to find plausible amounts in dungeons, or put it on display in your house.
Comparatively, it's like why many people want weight to have decimal values. When the smallest unit is one "feather", then you have pieces of paper worth one feather, and a metal helmet that either weighs the same as ten pieces of paper or you have to drive it up to crazy numbers and make the player's weight capacity something like twenty thousand feathers in order to accommodate all the inflated numbers. The decimals are just easier to deal with. So, basically, I'm saying the opposite; it makes things less complicated, along with simple factors of realism.