The amulets were removed on purpose, and there's no indication that they will ever be restored. The only amulets left in chests were those that could be made the only things in the container (Chantry-related valuables were removed from the chest in the Fallow Mire, Blackwall's amulet is alone on the corpse in Adamant, and the player amulet is alone on the ground in Crestwood now); all other lootable amulets were removed from the game (even if they weren't ones that could be exploited).
It seems most characters should now have access to only 2 amulets, though there seem to be exceptions (all of Dorian's got removed, as the only war table one he gets is unfairly hidden in a totally unrelated mission that requires you to recruit a different companion, raise approval enough to trigger their quest, complete their quest a certain way, and then perform a convoluted chain of war table operations to hopefully get the amulet).
However, if BioWare decided to add them back to their original locations, it wouldn't be retroactive if you'd already looted the chest or killed the creature where the amulet should have been found.
Hopefully they'll at least add another amulet for Dorian somewhere, though I have little hope it would be helpful to most people whose games are already in progress.