Yes, exchanges are hacked periodically (or just scam on their users like what Cryptsy did), but if you are a day-trader (or close to being that) you may not have any other option apart from keeping your funds in your exchange account. Until distributed decentralized exchanges kick off for real (if ever), you have to either risk your money being stolen by hackers (exchanges themselves) or stay away from Bitcoin trading altogether missing out on a lot of good opportunities to earn decent profits.