Nook SimpleTouch rooted, can I manage Shelves now? -- sounds like you can root and use the
Calibre Companion app. If you get a ROM which has android 2.3 for Nook. I'm sure there is one out there.
How does the Nook ST handle collections? -- send to device in calibre so the books are in folders, and open them via "My Files" instead of "All Books", since it will show folder view.
Unfortunately, it seems that there IS no way to just create collections automatically, and also that collections will be emptied if they have books from the MicroSD card -- every time you reboot it. Which makes it sound as if Shelves for the Nook are somewhat pointless.