Hello Tyro,
Yeah, Right now the game doesn't have a Tool shop, but I think that was a mistake in not adding one.
I’m working on an update, and a I’ll try to add the Tool shop in that update.
As for the map generation, right now things are a little bit random, where in some worlds shops won’t appear, and there are dead ends/unreachable areas. But, this is something I might try to make a little bit better in the future.
I kind of would like to make the NPCs intractable in the future. So they will have more of a role in the gameplay, but that is something that will take a while to get working.
Overall, I think your right that the game needs some tweaking in different areas, including the shops/item stacking/NPCs.