Seems like this is just an extension of any other dispute, and failure to resolve conflict between neighbors, perhaps due to lack of community cohesion between the store owner and yourself or others. This is the nature of living, and if there are problems, we should have ways to resolve it without crazy blanket rules like no commercial next to residential. The failure is in the reasons become homeless and in responding to people who actively disrupt the peace and intrude, not the existence of a store.

It's not just that it's not a fundamental characteristic of stores, but it's also not a fundamental characteristic of homeless people, it's just a characteristic of these homeless people and this store. Depending on the type of store, I'd grant you that other issues could have arisen, such as rodents, smells, etc.. but also any other neighbor could be hosting parties, smoking near your window, leaving debris around. In some cases, you either need to accept it, adapt, or find somewhere else to live.

I had a neighbor in the burbs growing up that didn't like the way we behaved on our property, or how it looked, and stuck her nose in and intruded frequently, often threatening to call the police for all sorts of absurd reasons.

If a house near you were abandoned, could you do something about it?