Because all songs in iTunes Store and Apple Music have sample rate of 44.1kHz.
I am not confidant that I can tell the difference in a double-blind test but I am sure that aTV 3 has pretty poor sound quality. I think this unnecessary 44.1kHz->48kHz resampling is one of the reason.
Restated: Why does the AppleTV resample all the iTunes Music Store and Apple Music to 48KHz?
Because it's Video oriented device and the TV and Movie industry, generally, has adopted 48KHz as the sample rate for audio tracks for Video media. There are some higher sample rates, but they aren't specified to play, in the native sample rate,on the AppleTV at this time.
Remember, you can use an AppleTV to output it's audio to an Airport Express (or multiple AirPlay renderers). In the case of playing your HomeSharing enabled account, iCloud Music, iTunes Music Purchases, iTunes Match Library and or Apple Music Account AND you want a 44KHz Sample Rate.
I agree with you; about the AppleTV 2/3 Sound quality, it's not as enjoyable to me as the optical output (and even Analog output) of the Apple Airport Express. I'd venture I wouldn't be able to positively identify a certain sample rate with repeatability. Still, before I knew about these technical details I always felt that the AppleTV (all versions) was not an idea audio device. I prefer the Apple Airport Express for Music listening.
Now, if you truly seek higher bit-depths and sample rates, the $499 MacMini does it all. I mean all. Every streaming service, Over-the-Air TV, 24bit, DSD, MKV, and anything else you can throw at it. It's a computer- I know. Paired up with a the Apple iOS Remote app, I don't think you'd miss out on Siri voice commands (found on AppleTV 4-- and projected to come mid-2016).
Further, using the Apple App Store approved BitPerfect ($25) allows you to use a variety of the highest quality Sample Rate Converters created.
There is always a way, it's how much time and money you want to spend.
