You are mixing and matching things.
Windows Home Server is built on top of the server side of Windows - optimised for... well, serving!
An atom may be a little slow, but will do what you need.
On the other hand, I am not sure of to many atom mother boards that support HDMI, and the ones that I do know do not have a pci express card so you may run in to a few problems.
That being said, if you do find one, there is nothing stopping you from using Windows home server and possibly installing a media program on top of it (it is possible to get out the gui and use the shell) but it is not recommended as the performance will most likly be bad on a atom.
If I was you, personally, use this as a nas, and buy yourself a descent a media extender such as the Netgear EVA range.. or even a second atom machine (if you find one with hdmi) and run one of quite a few Linux based distros designed for media such as http://geexbox.org/en/index.html