The problem is that Vayne spikes too early into the game. Through a combination, of Fleet Footwork, Overheal, and Targon's, she quite literally bypasses her supposed "weak early game". No matter how much you bully her in lane, she will eventually heal up to near full HP pretty easily. Vayne hits a massive powerspike by the time she buys two items.
According to League of Graphs (which has analysed over 9 million games since 8.1 hit live), her pick rate is high, her ban rate is high and her win rate is high. Those three factors indicate that she is out of line. She's getting nerfed because she is objectively too strong. It's the same reason why Evelynn and Malzahar are getting nerfed.
Win rate isn't everything though. Take Aurelion Sol for instance. He's mid's highest win rate champion. However, he isn't getting nerfed because he has a 1-2% pick rate, meaning it's only his mains that play him. If his pick rate spiked and his win rate stayed the same or increased, the chances are he'd be looked at himself.
Vayne is a high skill cap champion. Her win rate is supposed to be naturally low (especially if her pick rate is high), much like champions like Lee Sin and Azir (who both have 47-48% win rates at the moment).