There are several reasons behind department stores and discount houses operating this way.
For one, department stores are typically selling specific brands, so they are demanding a higher price point for a name brand, which has a bit more intrinsic value.
Another reason is that department stores tend to have higher costs associated with them than a discount house—they are in nice malls and offer a more pleasant shopping experience. This all translates to a higher cost and necessitates a larger margin than a discount house.
A final reason department stores mark up higher is the opportunity for emotional purchases. When they are marked up 30%, they can discount the product 20% and still make a good profit, but the customer feels like they are getting a deal because they see the markdown. This is a very standard practice with department stores.