I immediately unmounted the drive and ran debugfs and lsdel but it shows 0 inodes being deleted but the files are indeed gone.
Indeed they are. Consider the files gone and irrecoverable. If you still want to try, there's the forensics approach. Check any major "undelete" thread for steps. Understand beforehand recovery will be costly as in learning curve and invested time and comes with no guarantee wrt (partial) results whatsoever. You do make backups, right?..
The file system is ext3 and home is on its own partition. Not all of /home/user is gone.. just a few important directories. .thunderbird being one.
Ext3 actually thwarts recovery but that's in the gory details.
Does samba do something strange with it like put it in a recycle bin somewhere?
No, AFAIK it doesn't. If you want a thrashcan you could try and LD_PRELOAD something like
http://freshmeat.net/projects/libtrash/.