The rate of consumption is intended that way.
With different versions the amount each cup gives was changed, but the decay rate was also changed so that the overall rate of consumption of cups stayed the same. I did the initial balancing calculation so that a subfactory with six plantations can fuel one player permanently, which hopefully is still true.
Lowering the rate of consumption would lower the logistic hassle, that's true. However this hassle is part of the cost you have to pay in order to get the bonus from the caffeine. Without this cost, I might as well transfer the bonuses from a consumable item to a passive effect from the technology.
In short, the logistical problem of consumable coffee is intended as part of the cost you pay in return for the crafting and running speed bonuses.