When Inventory Setup Option "Automatic Cost Posting" is selected the usual case will be the COGS will posted automatically , but if the item is not in stock on the time of creating the Sales Order the COGS line will not be posted with sales invoice

i suggest to add an action to the posting to check if cost is available in the time of posting and then included if available

other wise accountant have to run the batch job every day to make sure their COGS Amount is always correct , where in other system it will always come if the item qty is available (like GP and AX)