i don't like the current mount system either. maybe horses and wargs should not be a resource that can be harvested infinitely but instead provide a fixed pool of mounts per site. for example, a stable allows you to train 1 unit with horses and a ranch (upgrade) allows you to have two cavalry units. when one of the cav units dies or is disbanded, you can then build a new unit with the horses (basically the same system civ 5 uses for strategic resources; also similar to how the dragon lair and ogre lair improvements in FE already work - an ogre lair spawns up to 3 ogres over time and will only spawn more when one of the ogres is deleted/killed)
this way, your ability to use mounted units would be more limited and you'd need more than 1 wild horse/warg site if you actually want to field armies that consist mostly/entirely of mounted troops.
I see what you want to achieve with this, you want to avoid huge stocks of horses by changing the sources from unlimited to limited.
What about requiring stock buildings instead? Let's say that a city can keep only a small amount of horses, like 10 or 20, and if you want to stock more horses you need to construct a city building, like for example stables, that makes for additional 10-20 horses.
And yes, horses and wargs should have a small upkeep cost. They are not paid wages, but they have to eat and be maintained anyway.
Another solution would be to require a new horse each time a unit is "healed from death". I will explain with an example: You have a group of three mounted units, and one is killed in combat, leaving you with a group of two units. Over time the group is healed and one unit "resurrects" or more apropiately, it's replaced by a new soldier. This soldier has a new horse, and this horse should be substracted from the stock. And by the way, it should be the same with material and crystal.