> So it's actually the same issue in minecraft

No. Take a look at the tool recipes. This is far less abstract - the handle of the pickaxe is just that long, hence two sticks.
Certainly, in Clonk, you could include a complex reasoning in every object's description. "Explosive arrow pack - Explosive ammunition for bow and crossbow. Needs 5 wood for the arrow shafts, one metal for..., sulphur for..., yadda yadda." Does that speak for itself, like the visual recipes?

> Why would a pickaxe be made of more than one stick? Why would I put something else than one metall on said stick?

The exact amount of each ingredient is somewhat arbitrary (e.g., crafting a brick block takes four bricks, while a diamond block takes nine diamonds), even more so in Clonk. However, in Minecraft, what you draw is what you get. With just one stick and one piece of metal, how could you distinguish between a shovel, a pickaxe, and a hoe? This is a big difference from the way crafting works in Clonk, where you choose the end product in a menu, and according to that consume materials.

> What I get is that Minecraft and Clonk use exactly the same system

I don't see how they are "exactly" the same. Apart from "building objects needs materials", I see little similarities.