Shinnok did become ruler of the Netherrealm when he defeated Lucifer and he is an Elder God afterall. It makes sense that if he can make a new body for Mileena and Sindel, then he can do the same for Scorpion.

Oh... when did that happen?!
Are you just making things up?

If you read the backstories in the official MKM: Sub-Zero website, it talks about how Shinnok overthrew Lucifer and became the new ruler of the Netherrealm.

As stated already, Shinnok was the one who gave Mileena a new body after her death and ordered her to spy on Shao Kahn and all.

Shinnok was the one who helped with Sindel's resurrection by tainting her soul with evil and reincarnating it on Earthrealm.

When it comes to Scorpion, like I said, if Shinnok can create new bodies, he can do that for Scorpion as well as Noob Saibot.

Well, that's VERY interesting!

Okay, and Mythologies is set before the first tournament, isn't it?
Mythologies is the MK I completely missed out on, so bare with me.

Sub-Zero double crosses Shinnok by the end of Mythologies, doesn't he?
If that's the case, I guess it's entirely reasonable to assume as ruler of the Netherrealm he would grant Scorpion the status of spectre to go kill him.

Then as Noob Saibot, well... that doesn't even need much explanation.
He was his servent...

... wow, that puts an entirely different spin on things.
It plays nicely into a post I made a couple of days ago, about the Netherrealm having a greater structure, too - ie. someone to bargain with to become a spectre.

Yes, MKM SZ took place 2 years before MK1 and it somewhat sort of retcons one little thing, but it's not really a big deal. It has to do with Sub-Zero's reaction to Scorpion in the MK1 comic when Scorpion finds him since Sub-Zero and Scorpion fought in the Netherrealm. Then again, I guess it has to do with Sub-Zero being surprised that Scorpion was actually able to appear in the living world so maybe it isn't a retcon. *shrugs*

As for Sub-Zero and Shinnok, well, Sub-Zero didn't really double cross Shinnok. In fact, Sub-Zero didn't even know about Shinnok until Quan Chi took Shinnok's amulet after Sub-Zero defeated the fire god and mentioned Shinnok to Sub-Zero. Sub-Zero defied both Quan Chi and Shinnok and like XiahouDun84 speculates, the ultimate punishment Quan Chi and Shinnok gave to Sub-Zero when he died is to make them their dutiful slave.