As when WordPress getting more and more popular, upgrading more than one WordPress can take up lot of effort and can not be done loosely. Web hosting companies who provide hosted WordPress, particularly find it hard to manage all.
In the other hand, CPanel provides a quick way to manage multiple web hosting account in one server, but also means less technical handson on the backend of your server. I personally prefer running and managing my server without a third party control panel such as CPanel.
We have done an installation of single WordPress to support more than 5,000 Blogs. We use MultiBlog script, modified and it works greatly!