Most folders will, but anything you copy back on from a backup or install has the chance to have .DS_Store files that will not be changed to the defaults until you make them change.
Thankfully it is easy enough to do that - in the same View Options pane, hold option and Use as Defaults changes to Restore to Defaults, and since Tiger this has even included sorting preferences! If it is detecting incorrectly, you may have to make some change to the rogue settings before that restore button becomes enabled.
Unfortunately this still doesn't work to set a global preference for window size, one of my favourite things that Windows 7 does better.