Currently we are writing the monthly update in which we will elaborate on this. Good to know for now:
Transactions can only be send with a passphrase. It's super important that you keep it safe and also create a 2nd passphrase and keep it offline (cold storage) to sign transactions. That's why the 2nd passphrase option is created. Because you all have the 1st passphrase inside your config.json on your server, and a server can be hacked if you have other ports listening, no secure password, and other possibilities of course.

Shift is not hacked. Our code is secure, we (and other parties) triple checked it. If our code is not secure, Lisk would've been hacked too and there's lots more $$$ involved there. We strongly recommend you to create a 2nd passphrase at all times.