The main drawback (or advantage, depending on your point of view) of using Linux as an HTPC is the lack of support for DRM sources, such as Netflix and Bluray. However, Amazon keeps adding more content to their video on demand service, and there are many other online streaming video sources that do work fine with Linux.
As for TrueHD and DTS-HD, yes I watch movies ripped to .mkv format, and those audio formats work fine using MythTV with an nVidia GT430 video card. If you're just watching ripped content, and not using your computer as a DVR, then XBMC would be a better choice than MythTV, but I don't know what the current status of HD Audio is on XBMC.
Which reminds me, if you haven't bought the hardware yet, make sure you get an nVidia video card. ATI and Intel aren't adequately supported yet in Linux.