It's one of the weaknesses of the Shield audio mixer that really bothers me. All PCM gets upsampled to 48k. The DTS CD isn't PCM, but a bitstream, so it gets passed along unchanged. I wish there was a PCM passthrough or exclusive mode (e.g. Windows WASAPI) but there doesn't seem to be one. To be fair though, I haven't heard an audible difference after upsampling. My sense of rightness is offended just knowing it's not the original.
I thought DTS CDs were encoded in plain PCM (hence the WAV files). KODI won't even play DTS Wavs wrapped in ALAC, though (you just get noise). My 1st gen ATV would play them without even knowing it as it just played them without touching the unwrapped signal. It also played at the correct sampling rates. Amazing how a box from 2007 does it right, but on you buy in 2019 screws it up....
If KODI can recognize a DTS signal in a WAV file and and send it out in untouched, I don't know why it cannot do the same for all PCM audio. This probably explains why I cannot play a dump of my Auro-3D movie Red Tails, however as it encodes the Auro -3D signal in plain PCM. No passthrough setting will allow it to play correctly. Yet it IS 48kHz already so clearly the NVIDIA mixer is modifying the signal (or KODI is). Yet my other Auro-3D movies that wrap the encoded PCM signal in DTS-HD Master Audio decode just fine from KODI.
I posted that at the KODI forums. They ignore me there 100% for insulting a developer who was being so nasty to some poor guy (I thought it was a private comment to the guy, but I guess it wasn't. The developer guy (whose first language is German, not English and probably why he misunderstood the guy but insulted him three times anyway) hasn't gotten over it four years later (my warning level is a permanent 100% there while those guys talk down to everyone at will. They even banned their own web guy from blocking a developer from attacking another one.
I can't say I like most of Team KODI much, but it's free so that means no complaints ever. I'd rather pay and have some recourse and feedback/suggestions listened to rather than be told to let them know when I've added the code (e.g. There is still no tag reading for M4V (MP4) video files 13 YEARS after Apple added it to the first Apple TV! The music tag reader can actually already read the video file tags, so a little cut/paste and sorting of the tag code could have had it added probably within a day or two, but they have literally ZERO interest (We would probably have better MKV tagging software by now if KODI supported tags there as well). We've had music tags since the late 20th Century, but are stuck with archaic naming based scraper/database with videos in 2019 still...RIDICULOUS IMO.