You can prevent spotlight from indexing certain folders by going to the "privacy" tab in the "Spotlight" preference pane in the System Preferences app. You can use this to add specfic USB drives to the list of things not to index. That should get rid of the .Spotlight-V100 files. This is not a generic solition for "all drives", but has to be done specifically for each drive.
As for not creating .Trashes files. I don't think that's possible. That's how OS X deals with deleted items.
You can prevent spotlight from indexing certain folders by going to the "privacy" tab in the "Spotlight" preference pane in the System Preferences app. You can use this to add specfic USB drives to the list of things not to index. That should get rid of the .Spotlight-V100 files. This is not a generic solition for "all drives", but has to be done specifically for each drive.
As for not creating .Trashes files. I don't think that's possible. That's how OS X deals with deleted items.
I don't know of anyway to stop them being put on manually, but Blue Harvest is a tool that will do it for you.
One way is to create files called .Trashes and .Spotlight-V100
To be sure, do this from a Windows PC and make the files read-only. Just be careful that they don't get deleted.
When you try to delete files now, OS X will tell you they must be deleted immediately instead of moving them to the trash.