Does requiring cost centers affect automatically created journal entries?

No. The Require Cost Centers on Manual Journals option applies only when creating or editing manual journal entries, from Add Entry or when editing a manual entry. Other transactions, such as sales invoices, purchase invoices and requisitions, are saved normally and their automatic journal entries are created, even if they use one of the selected accounts without distributing it to a cost center.

To set cost centers for the items of sales invoices, purchase invoices and requisitions, turn on Item-Level Cost Center Assignment by Transaction Type in General Accounting Settings.