Hackers don't use magical tools that are not available elsewhere. Most tools hackers use were actually intended for other purposes.
Just like a knife is used as a cutting instrument it can also be used to stab people, that was not the use it was provided for. The same is true for many hacking tools.
Sometimes all you need to hack into a server is a knowledge of a bug in a piece of software, telnet clent and a port scanner to find vulnerable machines.
And yes the best way to defend against hackers is to think like a hacker. If you can think like a hacker you can then figure how to defend against a hacker.
