I know this is a big question, but I wonder if the widespread and unprecedented destruction on a large scale of those lands in the centre of Europe, through which many important and long-established trade routes went, had equally large effects on the european trade and trade networks. For example I know the Hanseatic cities remained neutral and were already in decline, but their final downfall seems to have come in the times directly after the war.
There was a commercial crisis extending from central to north-western Europe as early as 1620, during the conflict's initial Bohemian phase, though the slowing of silver shipments from the New World may also have contributed. Without questioning estimates of human loss, Schulze & Volckart consider the longer-term commercial impact over-rated (http://eh.net/eha/wp-content/uploads/2013/11/SchulzeVolckart.pdf), with trade diversion from war-torn routes (Leipzig seeming to be a major beneficiary, at least going by grain price movements - surprisingly for me as I thought it remained sluggish in population terms until a good deal later) but general revival by the 18th century.