It's unfortunate that you have had that terrible experience and that the legal system in your location failed you.

I'm not sure however that there's anything to indicate that mom and pop stores are especially susceptible to these kinds of outcomes. It sounds more like you got a case of shitty neighbour which is possible whether or not the neighbour is a commercial lot or a small home.

If your negative experience had been with a neighbour living in a private home instead of a neighbour who owned a small business would that change your view around the matter of zoning for small businesses in residential neighbourhoods?