In 4.2c and older, I was able to make Header (sub)items admin-only by enclosing items between <#if user.isAdmin> and </#if>.
For example the Create Site-option was editable like that in: tomcat/webapps/share/WEB-INF/classes/alfresco/site-webscripts/org/alfresco/modules/header/sites.get.html.ftl
Also, to make the Repository button admin-accessible only, you could set "permission=admin" to the right option in: tomcat/webapps/share/WEB-INF/classes/alfresco/share-config.xml
In 4.2d, these don't work anymore and I can't find where I can influence this behaviour.
Setting <legacy-mode-enabled> to 'true', which should make the pre-4.2d way work again, but this made things far worse: the Header bar layout was all wrong.
Hope someone can point me in te right direction!