Since version 3.5 of WordPress, the development team has removed the links functionality from the standard installation.
I don't know why but this is the status.
If you have updated your blog you shouldn't see any changes you should see the Links and the blogroll as in previous versions.
If you are going to create a new blog as I did yesterday (www.svaporhouse.it with wordpress 3.5.1), you won't find the link manager.
It is very simple to install the link manager, simply click "Plugins->Add New"
Search for "link Manager"
Install the "Link Manager" plugin
That's all.