same way not many know that Naruto is the fourth hokage's son. And the very same way that members of "Root" can't so much as speak of Danzo. Covered up. Danzo is a high authority in Konaha. He could--with effort, cover up his activities of stealing a Sharingan.
But a missing Uchiha is a missing Uchiha. The village would be in an uproar. It's a risky operation for Danzo not just for the possibility of getting caught; losing the secrets of their great Sharingan to an unknown adversary would damage the position of the Hidden Leaf toward the enemy.
his orders were to flat out -kill- Sasuke.
Not bring him back, not fight him so that his sharingan powers are shown, but to kill him, even in his sleep if he had to. Madara wants to use Sasuke....can't use something that's dead.
Keep in mind that not all orders to kill are just that. Within Danzo's hidden agenda, anything from a test, a warning, or careful manipulation could be the real goal. The order to kill ensures Sasuke's adversary isn't holding back, but what if Danzo had always expected Sasuke to come out on top? Especially with Madara using Danzo as an excuse to get rid of the other Kage, Danzo's ordering to kill Sasuke is surely giving him a message of his existence, forcing upon Sasuke more hatred toward the Hidden Leaf. Naruto just messed up whatever agenda Danzo could have had beyond wanting Sasuke dead.
I still find the idea that Danzo = Madara silly.
Like I said, it's one of three scenarios. Danzo and Madara could be working together to a single goal, whilst trying to avoid suspicison of their allegiance, or Madara is really just using Danzo like a tool. The fact remains that Madara is playing wonderfully on whatever Danzo has done and Danzou is taking equal advantage of Madara's actions.
Needless to say, now that Danzo is hokage--if he was also Madara--he could easily make Naruto disappear and into the hands of Akatsuki without many being the wiser.
They still need the 8-tail before even bothering with Naruto.. Aside from that, Madara on his own could have taken Naruto long ago. It just comes to show how much more involved Madara is with the careful progression of his big plan instead of getting the last of the tailed beasts quickly.
I'd like to add that it would not have been that difficult for Danzo to get the Sharingan. He could have simply had it plucked out from the guy that Itachi killed to obtain the Mangekyo Sharingan.
But Danzo had the hidden eye long before that.