First off, have you ever used a rake? If you can, go out to the back yard, grab a metal rake (not a grass or leaf rake) and slam it into the ground and pull.. it will bring up a chunk of dirt. Keep at it and you can dig a hole. I grew up on a farm for some years as a kid and did plenty of this stuff. Unless the dirt is mostly sand, then yes the rake will gather up dirt into a pile if that is your intention. Of course if you just drag it on the surface it won't do much...
So with different biomes.. these tools might have different affects (rake won't work the same in the dessert for example, it would barely smooth the surface)
I assume the pickaxe will stop working on dirt at some point since in reality it would just puncture holes into the ground and tear it up a bit, unless you hack away at it for an hour or it's some serious clay soil. Still would need a shovel or rake to get the dirt out of the hole.
Shovel, is there one currently in-game? I haven't seen it other than on the loading screen haha I guess what needs to happen is. Bring a shovel into the game. Stop the pickaxe from affecting dirt, and the shovel does the same as the pickaxe currently to dirt.
Still my suggestion is valid.. It just doesn't make sense that if you remove dirt with a rake that it just disappears into the void. But getting no stone with a sledgehammer does make sense. If you smash stone it kinda turns to dust... maybe stone dust could be collected and used for something? Maybe mortar?
So...
Pickaxe - stone/ore collection
Sledgehammer - stone smoothing (stone dust collection?)
Shovel - dirt collection (maybe there will be something found in dirt to be collected which is useful to the player?)
Rake - dirt smoothing (just add the suggestion above)
etc..