IRC is a multi server protocol in that you can use multiple servers to run one IRC network, consider it like load balancing.
So as to why the majority of projects are on there is not a question with a simple defined answer. First of all, there are other IRC networks which host projects too, OFTC being the other big one.
Why are the majority on Freenode? probably because it is one of the bigger longer running IRC networks and if it has the majority of users then you want to have your project channel hosted where the largest number of users are, hence Freenode.
Perhaps the project creators were already users of Freenode and for ease of use continue to host their channels on Freenode.
Hosting maintaining and moderating an IRC network is no small task and for the majority of smaller projects, the time lost to chasing these issues would be better spent working on the project itself.