So, when Sub-Zero (Kuai Lang) was captured and turned into a cyborg, he lost his soul, right? This was explained in MK3 since Cyrax and Sektor were immune to Shao Kahn's invasion, as their souls could not be absorbed since they had none.

Perhaps Cyber Sub-Zero "regained" his soul after being reprogrammed, fair enough, but why would he show up as a cyborg in the Netherrealm? Shouldn't he have resumed his human form (although dark and zombie-like?)

I am starting to wonder now if Noob was destroyed by the soulnado in MK9 and perhaps "purified", thus returning to human form, free of Quan-Chi's influence, whereas his brother's soul still belongs to Quan-Chi.