[eluser]xwero[/eluser]
The libraries in the system directory could be seen as the core libraries because that is where the core libraries are but there are not going to be problems if you add a library of your own. My rule is if the library is used in multiple apps put it in the system directory else put it in the application directory.
No plugins are not hard coded to contain a single function but if you add more functions then you wipe out the difference between plugins and helpers. I don't say you shouldn't do it, it's just a matter of preference.
The technical difference between plugins and helpers is the directory where they are stored, the plugin has to have a _pi.php extension and the helper can be extended.