NAD displaying different kHz than Roon when playing an MQA file

I am playing MQA through NAD 758 v3. Roon identifies TIDAL FLAC 48 kHz 24 bit 2 ch, MQA 96 kHz. On NAD display, 2/0.0 48k. Why the difference?

No difference.
Both say 48k.

In addition, Roon says that the file is MQA encoded so if you apply MQA decoding in the DAC it would become 96k.

You need to install BlueOS player in order to decode MQA. However, Roon is working on it and will release soon.