1) I meant a folder with the SKU... that way when you browse to a product you could go straight to that folder and wouldn't have to filter out any images since all of the images in that folder would be for that product.
2) You could do this however you wanted to. I'm just suggesting methods I've used in the past and don't know your specific scenario.
3) That seems like a valid enough reason to use a flat file solution rather than a database.