I can't answer you question with respect to the Sony devices.
The Kobo Touch can handle thousands of books, but shelving then is impractical from the device. The calibre driver will do this based on columns in the calibre library. How practical this is, I don't know as I normally have less than 500 books on my Touch. I actually have over 200 shelves and extra 500 books on the SD card at the moment while I test something. The first time i did this the setup of the shelves took a few minutes, but syncing now is a lot faster.
You should also reconsider the Kobo Glo. The front lighting is the main thing mentioned, but it has a faster CPU (1GHz vz 800MHz in the Touch) and a higher screen resolution (1024*758 vs 800*600).