Have buffer more by starting the KDE Control Center, and moving to the Sound group, and Soundserver section, and increasing the response time. 348ms is usually sufficient for most computers. You may also consider running the soundserver with real-time priority if setting the response time doesn't help. Be aware that this can cause your system to lock-up.
Not every plugin puts an item in there. The ID3 plugin does, for editing the currently playing file's ID3 tag.
Since Noatun requires at least one user-interface loaded, and exactly one playlist, you have to add a new user-interface plugin before removing the old one. Adding a new playlist will automatically remove the old one.
Third-party developers can submit their own plugins to the Noatun web-site, where they can be downloaded by you, the users.
Documentation, an API reference, and example source code is available at the Noatun web-site. Also, in the spirit of Open Source software, the source code to Noatun, and all default plugins is available.