I speak from experience as I lived in a house near a guy who decided to do just that... broken down cars parked everywhere (leaking all sorts of stuff), noise at all hours.
Gotta be a balance between things.
Banning automotive repair might be ok by itself but there's another idiot who wants to ban X, and Y and Z and their complaints are just as valid as yours and the status quo is what you get when you try and accommodate all of them.
Depends on the store. I've lived next to grocery stores with the loudest compressors for refrigeration that I've ever heard. Going to take some nuance there.
Want to prioritize walkability to shops? Zoning is a great way to make that happen.
Want to prioritize keeping noisy things away from residential areas? Zoning is great for that too!
Want to make a socially segregated city? You can absolutely do that with zoning!
Zoning is a super great tool, it's just that the things it optimizes for are sometimes misguided (or in some cases straight-up harmful).