'decrease in custom' vs 'decrease in sales'

Custom refers to “regular dealings with a shop or business by customers” so could be taken to have a somewhat broader meaning than sales, although I suspect that the intent here is largely a desire to keep the language from being too repetitive. A large part depends on the context. In a technical document (e.g., a government report), it's more likely to have a significant difference in meaning than in something less formal such as news reporting.