Few reasons:
1. Soundblasters LIVE by Creative used 48KHz internal clock and it was perceived as a terrible move.
All other cards at the time supported 44.1KHz, 22.050Hz, 11.025Hz... and they were targetting CD Audio quality because CDs just made it as a PC peripherals with highest amount of content at that time. MP3 started to became a thing and again 44,1KHz was a target... This is ofc history from 1998, but EAX 1.0 and 2.0 were expected to become as important as were graphical Shader Engines and back in that time, audio accelerator made similar sense as 3d accelerator.
So, if an engine used EAX effects it allowed higher CPU performance by about 10 percent, however at cost of intermodulation distortion - because majority of older titles were developed with CD Quality audio in mind as most older soundcards supported. Yet Creative was targeting different market with 5.1 support - DVDs and surround sound.
Also a reason why was so popular to use analog CD Audio passthrough instead on PCs digital processing with these cards.
But you actually made me think about the whole story a bit. This is the list of games with EAX support:
en.wikipedia.org
It would make sense if those are sampled in 48KHz, however if you would attempt to play that sound on a more common soundcards from that era, you would simply get a message that the format is not supported. Game developers were quite furious about that.
With Audigy series it was the first time they implemented options of using different sample rates (44.1, 48 and 96) and higher bitrates (16 and 24), yet that was all still on Windows XP. So the initial outrage was no longer a problem and Audigy offered a decent sound effects, with more common sample rate.
The problem was that no other audio card manufacturer went into DirectSound as it was envisioned by Creative and adopted by Microsoft. Later as CPU performance increased, there were software filters with similar capabilities, but without any need for specific hardware or DirectSound. Then Vista happenned, DirectSound was mostly scrapped, and Windows got the audiostack as we know it now. So up to 2006-2008 there was not much devices
2. I was involved in a game development back in 2006
All the sound was mastered for CD quality. But again quite a history since then. There was a strong opinion that 44,1KHz 16bit is enough.
Since then I have been checking around overclock and gaming forums and general consensus was that games are still using 44.1 16bit, however i doubt anyone checked...
So I just ran few audiofiles headers through my media players, and even when they failed to render, it seems Nier Automata is indeed using 48KHz.