Try this:
{#series_order:||} {Series_index:0>3s} {title} - {author} - ( Series - {series:||}){#series_order:| - (Series Order - |)}
If #series_order is set, it'll use the stuff marked by the pipes (" - (Series Order - " before the value, and ")" after). If #series_order is empty, it ignores all that stuff and everything between that set of braces is left out.
You could probably apply the same transformation to the series field before it, and leave that part out if the series is blank.
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