Wouldn't it be simpler to make all the hook methods public, so that plugins can register themselves?

Plugins already can register themselves. In fact, there's no reason to wait for Vault to be active to hook your own plugin, as long as the classes are loaded you can register your own economy into the services manager.

Oh, okay then. I was just wondering, why certain plugins are listed in the Vault source code.

Generally it's easier to keep all the hooks for the major plugins in Vault, that way they can be updated collaboratively, it's not a requirement by any means though. It also means faster updates to the hooks if I make a breaking change in the Vault API, by adding a method, since I will go through and add the method to all of the plugin hooks myself.