How can I tell the difference between numb patches on my feet caused by shoe/use compression or by more ominous causes?

Probably not shoes. A numb patch by a shoe is going to be either a callus, a wart (both easy enough to see), or go way quickly after the shoes are removed. Sometimes nerves can be damaged more seriously by long term compression, but i would never assume that is the case without a doctor knowing the whole story and saying that was it. The later would be rare.
Skin appearance. Shoe pressure numbness will probably be accompanied by skin color changes. Inspect your skin, also look for bony areas which may rub on the shoes. This without, probably won't have anything to do with shoes. Don't where shoes, and see if you still have numbness.