As Prima Italia said, Subz beat Scorp in MK9, and he beat him again in the MKX comic even though Scorpion had help from Takeda. So it's definitely not true that "in all lore battles scorpion beats sub zero."
The single time Scorpion won was in MKX, and yeah Scorpion technically won, but if you look at the actual cinematic, it's clear that Sub-Zero was not defeated. He was still strong enough, and aware enough, to freeze Frost and stop her from hurting Hanzo.
So in terms of lore, actually the fights clearly favor Sub-Zero.
P.S. you're kidding yourself if you think Sub-Zero is as popular as Scorpion.