They shouldn’t stack at all. Things that you can stack things on have a special tag for it. Unfortunately, they don’t seem to have working code for it. So you can stack any furniture.
This actually makes sense. It’s relatively easy to lift something up to head height and push it onto a shelf. It’s much harder to lift something above your head and then push it forward.
In the case of the pick, it’s actually extended your reach by the length of the handle. So of course the hearthling can use it to hit something a tile higher.
If you are only going on horizontal space used, you are correct. But there are a pair of advantages to large crates.
One Large Crate can hold 32 items for 2 pieces of wood. If you want to hold 32 items with small crates, you need to build 4 of them. That’s twice as much wood spent and more time spent crafting (due to carry times for the wood). And anytime you want to look in your crates, you have 4 times as many crates to look through.
I’ll build large crates every time to save on hassle.