The immediate thought is to use Metadata Navigation- one of the great features in SP2013 (ease of use, ease of management and consistency).
Unfortunately, in my scenario, not every user will have read access to every site/page/library in my site collection. Managed Metadata Navigation- as of 18/07/2013 does not provide security trimming! What is the point of users being able to see links to resources they cannot see? When they click on one of the links they do not have right to access, they will see an 'Access denied aspx'. I have a strange feeling that they will not like this.
According to one saying: 'Out of sight, out of mind'- we will have to stick to hard-coding our links in headers in Site Settings -> Navigation (in order to see this link in Site Settings you have to activate Publishing Infrastructure Features both in Site collection and site levels):
Unlike with using Metadata Navigation (up to 3-tier dynamic menu allowed), we will be limited to Headers (links of their own) and Links below them (2-tier dynamic menu):