Some nuance on language.

Shop: wiktionary: From Middle English shoppe, from Old English sceoppa (“booth”)

1. An establishment that sells goods or services to the public; originally a physical location, but now a virtual establishment as well.
2. A place where things are crafted; a workshop or hobbyshop.
3. An automobile mechanic’s workplace.
4. Workplace; office. Used mainly in expressions such as shop talk, closed shop and shop floor.

Store: wiktionary:  Etymology from Latin instaurare – (“erect, establish”). store

1. A place where items may be accumulated or routinely kept.
2. A supply held in storage.
3. (mainly North American) A place where items may be purchased.

A shop is a place where things are worked on (and sold), a store is a place where things are kept (and sold). We go shopping but we don’t go storing, we come home and store the things we got from the larger store.

The idea of a store, where things that we may need are stored and distributed, is ultimately one of sharing community resources. I may need tools at some point, but rather than own all the tools I might need, there is a hardware store which sells things on a just-in-time basis to consumers. Who owns the hardware store (an individual, a firm, a cooperative) is secondary to the necessity of such a function to achieve economies of scale and ensure variety. If there were no stores, we would need to store everything we might need, and would need to truck and barter for goods with their makers, a much less efficiency system.

The idea of a shop is just the place where the trade takes place. Implicitly, a store holds lots of things, a shop is just a place for the transaction or some local repair work. This is somewhat lost in modern usage, but we still have hardware stores and grocery stores (which are relatively large), but dress shops, tailor shops, auto shops (which at least the first two are relatively small, and the latter two refer to where things are done rather than already made things are sold).

Both of these functions are necessary in urban systems. We  need both places to store items we may need in the future (and then acquire them when needed), and we need shop-places to work on things, making them, repairing them, altering them.  With the move toward a disposable society, where it costs more to fix things (which is a laborious process) than make them (which is often automated), the share of space devoted to shops rather than stores has declined. Proposition Joe is in a declining business (“Shine that up and put $7.50 on it… Shame to let a good toaster go to waste over a frayed cord” – Proposition Joe, The Wire)

Where these things are located relative to where people and live and work depends on the frequency of use. We want things we want frequently (e.g. milk), to be closer than things we want infrequently (e.g. furniture). But closer and farther are relative not absolute terms. They depend on context: location with respect to others (density or community demand), the cost of travel (technology), frequency of use (individual demand), and so on. Relative locations have changed over time as density, technology, and demand have changed.

See also: Just-in-time consumption: Does the `pint of milk test’ hold water?