It might be worth looking at setting up a local directory as a handheld device, and have MC keep that in sync, auto converting to mp3 as required, and, though I'm not 100% certain, I'm sure you can then create a new library that includes only those files.
FYI - this is EXACTLY how I would approach it as things stand today. It would mean having a separate library for each re-encode/device and would take multiple syncs to keep everything up to date. Things would fall apart if the same files were being updated on different handhelds in one round of 'syncing'.
For example
Main library = lossless.
Create a folder (say "VBR") as a handheld and sync library to that as VBR encoded files.
Make 'VBR' library and set up iPod sync in that. Use that library to sync files to/from iPod and update ratings.
Periodically open lossy library and sync it back to 'VBR' library to update data in main libraray.
Repeat above for each compression level desired (like say 128kbps for a shuffle).
This quickly becomes a lot of work if like me you are still in the (seemingly never-ending) process of 'cleaning up' your data.