[Sirtel]

As for hiding items that are not downloaded, that's entirely possible. Just select Downloaded instead of All on the Kindle homepage.

As to your device per library question, I don't know that such a thing is possible. Calibre usually recognizes the connected device and handles most of the sideloading process automagically. For the first time your Kindle is connected, configure the available formats and other things you want (azw3 is better than mobi for sideloading) by right-clicking on Device -> Configure this device. You don't have to do it repeatedly. I usually convert the books I want on my Kindle to azw3 beforehand.

You can use virtual libraries if you want, each virtual library for a specific device. But you don't have to change anything once you've configured a device the first time. The same goes for metadata plugboards, if you use any. Once you've done it the first time, Calibre will remember it.