You are correct. It is 100% legal to buy and sell a device with FaceTime in Saudi. The reasons for the majority of devices being sold without FT is as follows.
Within Qatar and the UAE, all voip is licenced by one or two telecoms companies. As such, Apple would need to pay royalties for every device sold. It is therefore removed. So why KSA? Well the method for Apple to block FaceTime, is linked to the serial number. It is not done through actual location, or network you are using. KSA purchases most of their devices through the Apple distributor in UAE, which means most of the devices they receive have no FaceTime. Some stores, Jarir included, have often gone out and purchased devices from either Australia or the U.K., and sold them at a premium, due to FaceTime being enabled. Perfectly legal.
What in my opinion is not legal or moral, is the marketing of FaceTime on products that are known not to have it. This is however not done by Apple, as they do not market in KSA (regardless of how many apples and "i's" the store puts in their name.