While there is no evidence that her email server was hacked, she did have correspondence with Sydney Blumenthal, who's account WAS hacked, and emails from that account were published.[1] This, combined with the fact that Clinton's server didn't boast the best security (allegedly), and it's not a stretch to imagine that her server was hacked.

[1] https://pando.com/2015/03/20/exclusive-interview-jailed-hack...