Brian,
You asked,
"Is there a why to keep OS X from creating/using these folders on a specific device?
Oh and can I make it stop creating these hidden files/folders on my windows shares as well?"
Those files, which you can only see when looking at your flash drive on your Windows machine, are hidden files OS X makes to keep track of files/folders and the trash. Remember, you can put something in the trash before you empty it, which is what the .trash file is for. Any file starting with a "." is a hidden file, necessary for system operation. (Which is why it's hidden, so you can't mess with it.)
As far as I know, you can't stop OS X from creating these files on your device ,as they are necessary. If anyone else knows otherwise, maybe they can chime in. I'll do a bit of research on the sharing part, but I don't think you do anything about them.
Brad
17 iMac 1.25GHz 768 MB DDR Mac OS X (10.4.4)