The word “hack” often brings up grim images of a shady individual sitting in a dark basement pounding away on a keyboard as he siphons money out of people’s bank accounts and funnels the funds to terrorist organizations. In reality, “hack” simply means a “solution to a problem” that is not necessarily uniform, standard, or elegant, but it gets the job done. As such, there can be both good hacks and bad hacks.
For your server, a hack may be necessary at times to fix immediate problems you might have. For example, a program may have a bug in it that causes problems for your websites. Even if you file a bug report, you might have to wait quite a while for the developer to fix it. In the meantime, if you have the wherewithal, you can hack the program to make it work as it was intended.
The disadvantage of a hack is that you can end up with a real hodgepodge of programming. When it comes time to update, upgrade, or otherwise expand your services, you may find that your hacks can cause the updates to break or otherwise not function properly. It is therefore very important to know exactly what you are doing and what your changes will effect. If you cannot be sure of the consequences, it is better to leave the hacking to the guys in the dark basement.