You can configure invoice email delivery down to the individual customer, not just at the account level.

The Invoice emails option in the customer details section will show "Not configured" when the account wide email settings are off. When the account wide setting is on, the field will show either "Send automatically" when on or off. The customer setting can be updated via the customer edit dialog.

Edits can be done manually in our webapp, or via API. Visit the create customer API docs and edit customer API docs where there is a new email_delivery option to control this configuration.