Currently Refreshed isn't available through CreateWiki yet, it should be.
The logo and the drop-down menu are separate features. The drop-down menu is controlled by MediaWiki:Refreshed-wiki-dropdown and its syntax is documented on MediaWiki.org. If it's empty (the default), the little "arrow" next to the wiki's wordmark won't be shown.
The actual site logo is configured by MediaWiki:Refreshed-this-wiki-wordmark (for desktop/normal screen resolutions) and MediaWiki:Refreshed-this-wiki-mobile-logo (for mobile/smaller screen resolutions); see the documentation for details.
But yeah, having Hub on the drop-down menu by default seems sane and sensible to me.
Agreed with @ashley that Hub should be on the dropdown menu. What about the default logo? I believe there should be some sort of image placeholder created or have it support text, so I'll look for the upstream ticket/make a ticket upstream
We can set a default logo by editing the aforementioned two MediaWiki: pages on our Interface Messages Wiki. All we need is the default logo image created and uploaded somewhere public (maybe Interface Messages Wiki itself? That'd make sense IMO), then we edit MediaWiki:Refreshed-this-wiki-wordmark to point to the URL of that image (and ditto for the mobile default logo).
This way the Refreshed skin will always have a logo image set but local administrators are still able to override it with a different one.
Shouldn't a default logo image be provided inside of Refreshed source code itself instead? Currently Refreshed doesn't provide any, and it's be nice if not only SW wikis could have a default but other wikis have one too.