I've read horror stories on the net about companies going bust (people shitting themsleves when kraken went dark), and reports saying that people could lose bitcoins. How is this possible? The coins are on the blockchain so you can just collect the coins later, with the next, latest and greatest crypto exchange, right? Even if Kraken went bust, pffft.. who cares? Your coins are safe on the blockchain right?
As you have said, the blockchain has not been hacked yet, so these companies being hacked are likely due to inside jobs, whether sanctioned or not. I don't use Kraken, so I don't know how it works, but if Kraken has sole ownership of your private key, you will no longer be able to access it in case of a hack.
As far as I know, this data could be somehow manipulated if someone had more than 50% of the hashrate. However, it is very unlike to happen. If you are worried about your huge investment then hardware wallet is the best choice right now. As other people said, human error is the most common here. Hardware wallets help you not to expose your private key.
Actually, if someone had control of 51% or more of the hashrate, they'll be able to choose whether to accept or reject transactions, and they'll be able to double spend. They can't manipulate the blockchain as far as I'm aware.