I am currently playing all of the quests in order. And only using the cards that were available at the time. And with 2 core sets.

I also own the 2 Hobbit saga expansion. My question is this:

Should I ever include those cards in my deck building? And if so, when?

Over Hill and Under Hill released just after the darrowdelf cycle ended and On the Doorstep came out in between

Heirs of Numenor and Steward's Fear

If i were you i would probably use all hobbit cards for HoN but if you are being very strict, cant use On the Doorstep till Stewards Fear