For TrueHD, I would expect it to be difficult to tell, as my understanding is that it is very similar to DVD-Audio's MLP (making the decoding process relatively straightforward and thus harder to get wrong). In that case, it would take a real mistake in hardware or software development to produce an audible difference. DTS-HD Master Audio is apparently a real processing bear, though, which is why the only Master Audio decoding available today is in receivers or processors.

The biggest thing that I see as a potential benefit for HDMI v1.x versus the 990's 7.1 Direct input is PLIIx. There is still very little 6.1/7.1 content available on HD software, but a fair number of 7.1 home theater setups. With nearly all HD-DVD and Blu-ray players offering only 5.1 analog outputs (when they have multichannel analog output at all), the only way to use the rear surrounds is to split the signals from the surrounds of a player's 5.1 output. That's not exactly earth-shatteringly important, but it is a consideration. Also, the 990 remains very unusual in its ability to apply bass management, time delay, and channel trim to a multichannel analog input, so there are a lot of other home theater setups that are relying on the player for those capabilities.