The following code will let the workflow associated with the Incoming Email Enabled Library be started automatically when it is set to started when a new item is created.
$spWebService = [Microsoft.SharePoint.Administration.SPWebService]::ContentService
$spWebService.DeclarativeWorkflowAutoStartOnEmailEnabled= $true
$spWebService.Update()
My client is keen to know about any performance issues or limitations before setting it to TRUE.