They won't 'show up', but like any web site that you can download Kindle format books from, you can use the K3 browser (or any other browser) to navigate to ACD and download books from there. It's not clear that ACD is any better suited to this than DropBox, Google Docs, MS Sky Drive, etc.
It would be nice if Amazon would provide Kindle-specific integration for ACD, so that it showed up as an item on Kindle ("My Amazon Cloud Drive Items") that you could download directly from, sync reading position and annotations, etc. After all, at a certain point, they'll make money if you use up the free storage allocation. I'd certainly make use of such 'value added' storage.