MK9 indicates that a dead soul, in Hell, has the same appearance the character did at the time of death.

Sub-Zero's soul looked like a cyborg because he was a cyborg when he died. Jax's soul still had bionic arms, Kabal's soul was covered in scars and wearing the respirator, everyone was wearing the clothes they died in, etc.

Your second question is harder to answer because there's a big plothole in MK9 about that, where they ignored or changed the rules: Good characters aren't supposed to be able to exist in the Netherealm AT ALL. Nightwolf in particular was established in Deception as being so pure and sinless that he normally cannot travel there.

But Quan Chi was somehow able to trap his soul there when he died anyway.

Oh yeah I completely forgot about that, for some reason I thought that they might revert to their original forms, unless they were reborn/resurrected as a Spectre or Wraith of course.

I was wondering about the second part myself, I was wondering why the dead Earthrealm warriors were in the NR when only people with some trace of evil in them are supposed to be able go there. I hope NRS clears that up one day

They more than likely won't which is a shame because I would love to know the answer to that. Usually when plotholes appear in MK, they usually just want us to forget about them.