I wonder if this effects the stack sizes of chests too.
I don't see it in the config or data file.
That's why I use ChestStacks to have a multiplier of the stack size of the players inventory.
The players inventory is effected by Stack Size Controller already.

This mod does adjust stack sizes for Large Wood Box and Wood Storage Box.

The config\StackSizeController.json has the values for categories. The data\StackSizeController.json has the settings for each individual item.

I believe the original poster was referring to the stack sizes in storage containers, which it does.

Ok. I don't see where to set inventory stack size and chest stacksizes individually.
By now I use Stack Size Controller and Chest Stacks.
Cause when I first used Stack Size Controller I could change the inventory stack size but
the size of the boxes did not change.
Thats why I used ChestStacks too cause it multiplies the stack size of an item that you already have in the inventory
related to chests.

Ahh. So there is the stack sizes, and there is the https://umod.org/plugins/capacity-controller 

No. It's not about the number of slots, it's just about the stack size of items in all kinds of chests.

StackSizeController will change the inventory stack size of storage containers. For instance, if you set the stack size of wood to 15,000, that's how much will stack in one slot in a box. You do not need an additional plugin unless you want the stack sizes for player inventories and storage container inventories to be different.