Hello,
sta99y, in a similar way to youe BluRay player decoding the HD audio and sending over the multi-channel outputs, players can also decode to 7.1 channels of LPCM audio, delivered over HDMI.
In this case the amp does not need to be able to decode HD audio as this has already been done at the player, and the LPCM is the raw HD digital audio. It just does the digital to analogue conversion and amplifies it, (whereas in your case the player does the digital to analogue conversion and your Yamaha is being used purely as an amplifier).
The alternative to either of these is sending the losslessly compressed, (Dolby True HD or DTS-HD MA bitstream), HD audio to the amp over HDMI, where the amp decodes it to LPCM, does the digital to analogue conversion, and amplifies it.
Any of the above is HD audio, it's just where the various processes involved happen that is different.
Digital electrical or optical connections can only carry the compressed non-HD DD or DTS, or a couple of channels of raw LPCM, (my Sonos for example is connected to my amp like this and sends stereo LPCM to my amp). They thus can't support HD audio for BluRays.