I have no idea what I'm looking at here. We only have 1 catalogue, and there's no 'no entries' message for it. Maybe it's not a catalogue, but this is filed as a catalogues bug.
I've just fixed the layout issue you noticed for the next site update.
As for it showing the no entries message, that is a bit more complex. The categories and entries are displayed via blocks, so the block is showing a no-entries message, not the DOWNLOAD_CATEGORY_SCREEN.tpl template itself. I'd have to tell the code to set render_if_empty=0 on that block. But then there's what if no entries are shown because some kind of filtering is being applied - you would want to actually see that message. I think I'll leave that for templaters. It's not a bug to say there are no entries when there really are none there, it's just a matter of opinion whether to say it or not.
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#3495 - No entries message when using subcategories
As for it showing the no entries message, that is a bit more complex. The categories and entries are displayed via blocks, so the block is showing a no-entries message, not the DOWNLOAD_CATEGORY_SCREEN.tpl template itself. I'd have to tell the code to set render_if_empty=0 on that block. But then there's what if no entries are shown because some kind of filtering is being applied - you would want to actually see that message. I think I'll leave that for templaters. It's not a bug to say there are no entries when there really are none there, it's just a matter of opinion whether to say it or not.