Seems like that would really disrupt the flow of the game. Smashes aren't even that hard to pull off with the buttons.
I don't understand when you say that it would disrupt the flow of the game; in fact, I would say that it improves the flow a lot. It's not a matter of smashes on the c-stick. The most important use of a c-stick is for control over aerial attacks, such as being able to fade away with f-airs. Smashes would be secondary, because, like you said, they're easy to do with the buttons.
I really think they should, like Roko Jono said, include the option of using it as a c-stick. Unfortunately, Sakurai claimed that touchscreen controls are currently "not planned", and knowing the closed nature of Sakurai, he most likely does not listen to suggestions. (n fact, it actually says on the Nintendo website that they do not take suggestions)
This eliminates the need for more competitive smashers to buy a new 3DS just for the small nub at the top.