I've been spending time tracking items in the shops for my own curiosity satisfaction, and I've noticed that some items will appear only when that merchant's ciy is in control of specific regions. When that region is not under that city's control, those same items are missing. It also seems that some items will not show up when certain regions are under that city's control as well. It's proving an interesting task to track this.
I can confirm this. Something similar happened to me at the cooking guild. With mt sandy character she didn't have what I was looking for, i think it was dried marjoram, but with my windy mule it was there. Alegience definitely makes a difference in some shops.