When Naruto first learned Shadow Clone, he was beating his own body up to use it. He didn't look much into what it can do aside dividing his own chakra to make real copies of himself.Everything is plot.
He's used it so often but didn't realize gaining experiences of his clones. Don't see how something so glaringly obvious wouldn't be noticed.
So far, he used it to make diversions and amp his blows. Training=/=real battle since you are unlikely to learn in the heat of fighting.