In most AEM components I've seen there is a file _cq_dialog.xml that defines a Touch UI dialog to configure the component. However, when I export a component with a CRX DE package, it contains _cq_dialog as a directory with .content.xml inside.
Is there any difference whether the dialog is defined in _cq_dialog.xml or _cq_dialog/.content.xml?
No, there is no difference between the two. Both are valid serializations of a cq:dialog node.
However, the version with the folder has the added benefit of allowing you to put descendant nodes of cq:dialog into separate files.