What gets copied (and what doesn't) during a Target Mode copy?
Target Disk Mode just turns the whole Mac into an external drive. There's essentially no difference between doing that and taking the drive out and putting it in a FireWire drive enclosure.
There's nothing special about TDM that makes it not-copy certain files.
However, when using a cloning app, some files may or may not be included. These are usually just 'temporary' data, such as caches, or machine-specific files that the system will recreate if absent. There may be options in the cloning app to exclude other files.