With the several new luxury resources added, other luxuries need to deplete to keep the game balanced. You really can't have the cake and eat it here.
There are better ways to balance the game.
1) Happiness has never been a major problem for me; if u think it is a concern why not just make the unhappiness penalty more.
2) Resources should dissapear as time goes along. For example, Coffee was a major product of Yeman in the middle ages but after 1600s it should dissapear in Yeman as Yeman was no longer a major coffee producer. The same is true for incense, horses, dye among other resources
3) Resources should be made rarer in quantity.
I want resource depletion to be somewhat in your control though. If you don't work a tile, resources replenish, so you have some control over it.
Replacing and dissapearing/replacing resources is much more historical. Resource replenishment can still be implemented but only for a limited amount of resources such as Ivory, Oil, Coal etc
Replacing/Disappearing resources would overall make the game more balanced. For example if u want a civilization/city to dominate a certain time period without the civ becoming powerful for the entire game; the replacing resources would be a great option (examples include: Romans, Persian, Arabs, Mongols). Other than that, it will also mean that old resources that are no longer important as time goes would disspear. Meaning that silk, horses, incense could dissapaear make room for new resources as time goes on. instead of having horses in the 20th century; why not just have them replaced with Coal, Aluminum, etc. This would mean that you dont have to overflow a city with resources you can just simply replace it (if that what ur looking for).