My opinion on this matter, and the conclusions I've come to regarding Scorpion and the MK story...
1) The Penence Stare, IMO, would affect Scorpion, but not in the way you'd think. Scorpion is driven by rage and hate, but isn't solely fueled by the rage of betrayal. Scorpion is perpetually haunted by his own personal demons (inadequacy, fear, vengence, etc), as well as the memories of his former life. The PS attacks the guilty and makes them the feel pain of the innocent; against Scorpion, that added pain would only fuel him more and make him stronger.
Scorpion, or rather his former self Hanzo Hasashi, is "the innocent" that the PS would show him (he blames himself just as much as he blamed Sub and Quan), and his family and clan are "the innocent" as far as Scorpion's story is concerned. With Scorpion already being fueled by the pain they felt, and the pain he feels, setting his soul ablaze with more hellfire wouldn't hurt...just amp him.
2) I'm not sure what you mean when you say "Scorpion's soul isn't bounded to him" because it most definately is bounded to him. Scorpion's soul is his own, hence why those who use him do it through manipulation rather than through outright control. Scorpion has always been "the wild card" of the MKU (noted in MK3), and his freedom to do as he pleases is really what his story revolves around. This concept of his freedom is really where his power/strength comes from, and IMO is the reason he was created/exists.
(slight tangent starts here, but follow me...)
MKA made it clear that Quan Chi was the source of the corruption in the realms. It was because of him that Shinnok fell from grace and became the "devil," and so it also becomes clear that it was because of Quan that Scorpion also fell. Scorpion, just as Quan was always the source of the realms corruption, was always meant to be the the EGs chosen one...there Champion, and Quan Chi was the one who corrupted him and set him on a crash course with the rest of the MKU. Because of this, I would agree with you that Scorpion's soul is boundless...limitless in its potential. All things considered, Scorpion has more in common with characters like Raiden, rather than Subzero, or any of the other MK "human" characters.
Scorpion really reminds me a lot of Spawn in a way, as Spawn (iirc) was held back/held himself back by holding on to his human side for a long time, but when he shed his human bonds he ultimately became more powerful. Scorpion, while he did hold onto his "human" side for a time before MK1, declared that Hanzo Hasashi (who he was in life) was dead, and that all that remained was Scorpion. Scorpion as he is now, is the embodiment of vengeance in the MKU much like GR is in Marvel, and as such, his rage and his power have no limit. This is really backed mainly in MKA as in that game Scorpion's power was jacked up immensely since during that time it was the EGs who pissed him off and so he went on a rampage across Edenia.
Scorpion's rage is what makes him unique among the rest of the cast. His ties to the heavens and to hell also allow him to run the gamut of power that he does.
Keep in mind that I say none of this to say Scorpion is all powerful, or anything like that. Scorpion was defeated in his most powerful forms (MKD and MKA), and has been defeated a few other times in the past; but all of those who defeated him though were of a different caliber of character, and often were the focus of said story at the time (Liu Kang, Kuai Liang (younger Subzero), Raiden, Taven, Quan Chi, Drahmin and Moloch (the Oni Tormentor and Destroyer)).
(end tangent)
3) Like I said earlier, Scorpion has more in common with the gods (Raiden, Fujin, etc.) than any of the more human MK characters. This is most evident in Scorpion's relationship with the Netherrealm and how it is akin to Raiden's relationship to Earthrealm. When Scorpion "dies" he returns to hell where he is reborn; when Scorpion is in his "home" realm, he is more powerful. To those who say "GR is like a god so Scorpion can't compete," this is the rebuttal to that. "Scorpion" isn't human, and never was; he is an immortal spirit that exists to fight and avenge and that is his only purpose. Nothing stops him for long, and through everything he just gets stronger. The only thing(s) in the MKU that can take Scorpion out for good is a God, or some being or entity with God-like power. Everything else is just a nuisance, a temporary road block to his ultimate goal.
To really address what you were saying though, yes Scorpion can withstand the tortures of the Netherrealm, but IMO the thing to take away from that is that realm actually fuels him and make him stronger just by being there. The Netherrealm's "torture" comes in the form of decay...withering and twisting the energies of life and magic into something corrupt and horrid. The only things that can survive/thrive against that realms natural forces are corrupt gods, the Oni race (demons), and some of the dead. Scorpion kind of falls in his own category as far as this goes, he could easily be classified as any of those three things, but seeing how he is looked at in context with the rest of the MKU, it is safe to say he is an anomaly of sorts.
4) Shinnok's "torture" in the Netherrealm is a little fuzzy, as evidence points to that it wasn't the realm that was torturing him, but rather Lucifer himself and his influence.
From the official story:
"Shinnok was banished to this place of torment by Rayden. Upon entering the realm, he found himself immediately under attack by its then ruler Lucifer, as well as those souls he was personally responsible for banishing when he was an Elder God. Locked and shackled, Shinnok was helpless against his attackers. He would exist, tortured and tormented by the dregs of hell for thousands of years. Until he met Quan Chi."
Story found here: http://www.mksecrets.net/index.php?section=mkmsz&lang=eng&contentID=4010
As the story states, Shinnok was tormented by the denizens of the Netherrealm, and so it can be inferred that the realm itself had little to no affect on him. Later on in the MK story (MKMSZ and MKA specifically), Shinnok is shown using his power unabatted and free from the NRs influence, but regardless of this he is eternally traped there due to the EGs power and decree.
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To sum up my opinion in a few words, the PS would either have a neutral affect on Scorpion or would make him more powerful, as everything that the PS is, is what Scorpion is, and what he is fueled by.
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Edit: I also like to add that I read (here on Comicvine.com) that the PS doesn't work on the blind, or on those with more than 2 eyes. While Scorpion doesn't fall into either of those categories, he does in fact have NO eyes.
The eyes Scorpion is seen with in most instances are a part of the "mask" that he wears. Scorpion is truly dead, and is only animated through magical means, and he sees through those magical means as well.
If someone could shed light on this issue, and/or show some instances of GR affecting beings who don't or cannot see by natural means, I'd be grateful.
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