I am not sure how to hide them after the fact, but there is a lengthy explanation in Mac Help when searching for "hidden files" that may be applicable. It appears to apply to 10.4 and 10.4.1 only, however.
After performing a NetInstall or restoring Mac OS X from a disk image, you may see certain files and folders at the root level of the Mac OS X volume that are not supposed to be visible, such as etc, tmp, and var. This article explains how to prevent these items from becoming visible.
In Mac OS X 10.3 and earlier, these items are made hidden (invisible) by listing them in a file named ".hidden" at the root level of the Mac OS X volume. Mac OS X 10.4 and later do not use this method to hide files. Instead, Mac OS X 10.4 and later hide files by setting certain attributes in the files themselves.
However, in Mac OS X 10.4 and 10.4.1, these attributes are not preserved when you create a disk image. To avoid the issue, update the computer on which the images are being created to the latest version of Mac OS X before creating the images (it is the version of the computer running the utility, not of the image itself, that matters). The issue is resolved in 10.4.2 for Disk Utility and hdiutil, and in 10.4.3 for System Image Utility.
If you already created images, you can prevent these files from becoming visible on a NetInstalled or restored system by using the following steps to make them invisible on the source disk image.
Note: These steps assume that you are familiar with creating and manipulating disk images using Disk Utility or the command-line tools, hdiutil and asr. For more information about these applications, refer to Disk Utility Help, or the man pages for the command-line tools.
Create a disk image in read-write format, or convert your existing image to read-write format.
Mount the image.
Insert your Mac OS X 10.4 Installation DVD into your computer.
Open a Terminal window and enter the following two commands:
$ cd /Volumes/Mac\ OS\ X\ Install\ DVD/System/Installation/Packages/OSInstall.mpkg/Contents/Resources/
$ sudo ./SetHidden /Volumes/<mounted image> hidden_MacOS9
Note: Each command following the $ prompt must be entered as a single line. The value <mounted image> should be replaced by the name of the mounted image. You can also copy the SetHidden file from the Installation DVD to a local directory. If you copy it, be sure that you also copy the hidden_MacOS9 file to the same location. This file contains the list of files to mark invisible.
Unmount the disk image.
Convert it back to compressed format.
Scan the image for restore.
You can now use the disk image to do a NetInstall or restore.
This document will be updated as more information becomes available.
