After reading the restocking guide, I have been trying to restock from stores on neopets. But I noticed that the prices never seem to change even when the store does get restocked. Are the prices not supposed to change or am I just supposed to haggle very low? Has the old restocking system been removed?

Restocking still works, last I checked, which was 30 minutes ago. The prices of the old items in the store do not change even if the store restocks.

I don't know how the old restocking system works and I'm not a restocker, but I do know that the price won't change. You can haggle (a bit) so you'll have to know what is rare and has a higher market value than the price in the shop. (And be fast enough to snipe it away from the shop.)