Because when Sub-Zero was turned into Noob Saibot he lost all his human emotions and became a pure evil wraith. That he came to be Shinnok and Quan Chi's slave was his punishment for defying them. They turned him into exactly what he didn't want to be. Noob Saibot is now proud of what he is, so he no longer care or is even grateful to Scorpion.

so does shinnok decide what ppl become when they are sent to the netherrealm or something?

The Elder Gods decide your punishment if they send you to the Netherealm.

But Shinnok has the power to take it further or switch it up if he wants. Make sense?

Shinnok, at the time, was ruler of the Netherrealm, was he not?

Shinnok took over the Neatherrealm when he was banished there by the Elder Gods and became its lord. Any soul that get sent there after death is suppose to have done great evil while it was alive and is under the full control of the lord of that realm. Quan Chi served Shinnok in a similiar way that Shang Tsung served Shao Kahn, and was given the right/power to use the souls of the fallen. Quan Chi used this power to 'recruit' servents like Sareena to serve himself and the Brotherhood of Shadows to appear to serve Shinnok where in reality they still served Quan Chi.

When the older Sub-Zero died, he was sent to the Neatherrealm and was quickly drafted into the ranks of the Brotherhood. (It would be easy to see that almost any 'old-school' Lin Kuei warrior that died was most likely sent to the Neatherrealm and became members of the Brotherhood.) When someone dies, he/she most likely loses most of his/her memories but there is occassions those memories remain intact or are distorted. Even if Noobs memories remain fully intact, I doubt he was given much choice on whether or not to join the Brotherhood, since the sorcerer most likely had full control over his soul. That appeared to have changed at the end of MK4 and now Noob is free to do as he chooses but is now warped by his years in the Neatherrealm and his service to Quan Chi and Shinnok. (Besides, he was never the 'good' guy it was his younger brother that gave the Sub-Zero name that heroic reputation.)


Then again I could be completely wrong and all that I just wrong is bits and piece of my own over active imagination...

My theory on this matter is:

Scorpion is described as a specter, Noob as a wraith. Spectres in the MK universe may be spirits who keep their memories as to go on a revenge quest/ tie up loose ends on Earth, and wraiths lose their memories and serve the lord of the Netherrealm (previously Lucifer, currently Shinnok).