It's a pretty cool Godot practice overall, so first of all - well done!
The problematic part is the upgrading system, it seems pretty unbalanced and confusing. As far as I can tell, sometimes it's hard or even impossible to tell if an upgrade makes any difference at all (upgraded the throwing star at least 4-5 times) - and some other times while an upgrade helps a lot at first (the damage multiplier), seemingly doesn't do anything later on.
If you ask me, it would be worth to have another look at the codes and re-balance the system, I suspect that with a minimal effort, the game could reach its potential and become a very-very fun idle game.