Only if you jailbreak. It's not possible to play back MKV files off NAS sources (over any protocol - UPnP, FTP, SMB, HTTP etc.) with hardware acceleration on a non-jailbroken device, not even on the iPad 4. (Software decoding needs far too much computing power.)
"Thank" Apple for their absolutely silly restrictions regarding hardware acceleration. It's all their fault - this is why jailbroken apps (RushPlayer+ and XBMC) play back MKV's just fine over UPnP and, with XBMC, SMB.