So I just bought this and I see that all the God's power tables have 12 numbers on them, but as far as I can tell the highest level that can be achieved is 9 (Slaanesh).

Why do you think they made the chart go so high?

Sebly said:

Expansion potential. There's no other reason

Expansions most likely. Possibly it was allowed to go higher it eh early drafts of the game.

To fill the graphical design is another option.