Specifically for Sion, I think Armor Pen are better if you max Q. If you max E then W second, Hybrid Pen may be cool (typically, when you will be bullied and you'll just try to poke and farm from afar). But if you max Q, 90% of your damage output in lane will be physical anyway.
And for Nasus, I don't play him so I am not sure, but on paper, I think it is so much better to have bigger Pen for your Q than medium Pen for both Q and E that I would never use Hybrid Pen on him. Your Q will be the most of your damage, unless you're playing some strange Support Nasus and maxing the Armor Shred.
Generally, if you deal "hybrid" damage but with shares of 70% - 30%, it's better to take Pen for the 70% part, not hybrid, and you can have a look on champion.gg for the shares. According to champion.gg, both Nasus and Sion deal roughly two times more physical than magic damage.
This is not a perfect way to make your decision, because for instance you'll deal much more Physical damage in late game, but maybe in lane your shares are closer to 50-50 so it would be cool to take Hybrid Pen for laning phase, but as a rule of thumb, it still works pretty well.