Hi,
I believe that directory essentially acts like a recycle bin in a Windows OS. Deleted files will stay there until you manually (and permanently) delete them. I would guess that those .sd files are for services that you deleted at some point.
If the .sd files in your trash directory are very large, I would guess it is because you published a large amount of data and copied it to the server when publishing, rather than accessing it from a registered data source.
Hope this helps.