If you're going to be using it for music, I'd forget about HDMI. To me, it's just a pain in the backside. I use it when I have to, and that's about it. Your audio will be fine on optical or coax digital, of course.
I might suggest using a different format than .wav, though. Although one benefit of it is smaller file size, I find a more important benefit to be that of mp3-style file tagging. Those tags will allow you to sort and play your music based on artist, title, album, etc., etc. .wav does not accommodate those tags, and you will have to maintain your own directory structure and the file names will probably be cryptic. I have been using .FLAC for several years now, much as you describe, and it's been perfect. My wife can use it without complaints, if that's worth anything to you.
We also store movied and pictures, like you are going to do. It's very convenient for everyone.
Although I kinda shot down HDMI for audio only, I might suggest you reconsider the DVD/BluRay capability. I can play DVDs over my network, but not yet BluRay. I would like to be able to do that, but I need to upgrade the video card, and perhaps other components. If you don't go for the HDMI video card now, you might at least spec the rest of the machine to be able to do BluRay in the future. I use PowerDVD, and they have specs there for what's needed for BluRay playback. Just a thought.
Good luck!