This is what I've discovered so far.
Quit Aperture (and automatically generate previews) --> launch iTunes: iPhoto Albums show up in iTunes but smart albums all missing
If I proceeded to sync my iPhone with iTunes, it will delete all my photos off my phone because nothing is synced!
Quit Aperture (and automatically generate previews) --> launch iPhoto --> quit iPhoto --> launch iTunes: Smart albums correctly show up, and correctly 'ticked' to indicate it will sync.
I suspect this is a limitation of using a supposedly 'unified' iPhoto Library in Aperture, but it isn't listed in the "Using the Unified Photo Library" guide at http://support.apple.com/kb/HT5043?viewlocale=en_US&locale=en_US.
Effectively though, it appears to me to be a data loss bug in the current implementation of Aperture / iTunes Library sharing.
I've tried to import my iPhoto Library to a new Aperture Library to no avail.
I can't speak specifically to iPhoto.
But I know that smart albums work fine with previews in Aperture. But that could be because all my Aperture albums have previews, and thus items in smart albums have already had previews generated for them in other albums.
Do you have Aperture set to share previews with iWork and iLife or whatever the settign is? That's necessary.
Test functionality in a new user to isolate the issue. I had my library do something similar and in a new user it worked just as it should.
I Generated Previews in my Apeture Library. Photos > hold Option key and select Generate Previews.
Took a long while. But that worked for me in my situation. I'm using up to date Aperture 3.3 and iPhoto 9.3