Short URLs work perfect, XWiki generates correct links in pages, BUT some links are genereated with /bin/ part still.
Quick search showed some places:
1. XWiki Logo
3. "Welcome to your wiki" link in the Recent Changes Panel
4. "User Directory" link in application panel
5. Very top menu has some "bin" links e.g Document index, wiki, add/attachment, almost all items at Page menu
6. Main.WebHome: in Spaces lis all spaces have correct links besides Main Space.
7. Comments, History, Info, Attachments links at the top and at the bottom of a page (Only in Main.WebHome page)
8. PDF-export at page menu
9. More actions: both menu items
10. Annotations: 2 links
11. Welcome to XWiki link at Breadcrumbs (very first link to Main.WebHome)