I would very much appreciate knowing ahead of time if my order cannot filled as stated.
Because of it being online, I would tend to feel the shop would have the responsibility to communicate to their customer for any reason they cannot fill the order. How else would the customer know? I think it would be a bad business practice too.
It's a two way street. When the customer knows, "she" can then have the option to look elsewhere, see if it can be backordered, or make whatever decision "she" needs too concerning "her" project. It fosters good customer relations, which may lead to increased sales by recommendations/word of mouth, gains consumer confidence and develops good communication skills.