The .DS_Store files have a purpose: they remember information about the state of windows--where they are, the type of view, the position and size of icons, etc. If you delete them, all the windows will revert to your default view. This is the sort of stuff that was in the two desktop database files in OS 9 and earlier. If you don't mind everything reverting to the default view, go ahead and delete the .DS_Store files. They're invisible in OS X. The only real problem is that they can be seen by a Windows computer if you save folders to a network disk, flash drive, etc.