I'm not disagreeing, just playing Devil's Advocate!so i am sure someone will disagree with me here but....
there is really little "danger" with working directly with the /var/hda/files/ShareName directories vs. the samba share that i can see.
The biggest difference is when Greyhole "deals" with them. If you use the samba shares, samba logs the file write, greyhole sees it and makes it's copies and sym links,
If you use the direct share, Greyhole waits until the next --fsck is run.
I think using samba has some performance sacrifices during the file transfer from my experience.
If you DON'T use Samba shares, then the hooks that Greyhole has into Samba will not be triggered, so the files won't be marked for Greyhole to process them, don't think you? After all, Greyhole doesn't process the files straight away, it merely adds stuff to the Greyhole queue (ie adds it to the Greyhole DB), and that's where fsck will pick them up from.
I think the only way to know for sure is to try this:
1) Start with a system where there are no pending Greyhole tasks
2) Copy something directly a given directory that would otherwise be accessible via Samba (ie not doing things through Samba for now)
3) Check the Greyhole mysql DB to see if the task has been added for that particular file
If I get a chance soon, I'll try this myself and report back...