Is it possible to fit a 36 hole rim to a 32 hole hub? I recently had my rear wheel replaced because the old one was bent. Everything about the new wheel was correct except that the shopkeeper ordered a 36 hole rim instead of 32 one. Due to this he told me he had to fit a new hub as well. The problem is my bicycle came with high quality hubs and the one he replaced it with cost ~$3. My rear wheel is wobbling now and I suspect it's the generic hub. Buying a new hub will cost me twice the price of the wheel. Can I just reuse the old one with the new wheel
Theoretically? Yes. Practically? No.

the shopkeeper ordered a 36 hole rim instead of 32 one.

In most of the world this is his problem. You ordered new rim that will it your hub from him, so that's what you should get. Go to him, tell him you want what you ordered, that is a rim on your hub, or you want your money back and go to another repair shop  to make your wheel. If he opposes, then it is a question for sister site, Law Stack Exchange. But if you are in the European Union shopkeeper is on a losing position. I believe that's the case for most of the western world.