Adding links to $content['links'] in theme layer I know that I can use template_node_view_alter() or template_preprocess_node() in template.php, but the problem is, that some of the information that I can alter there, seems to be processed already. For example:

$variables['content']['links']['node']['#links']['node-readmore']['title']


have some styling informations and a bit of text that is already translated. Is it possible to add a link even before, that structure was constructed? I don't want to overwrite something that was generated by Drupal for specific purpose.
You don't have to worry about overwriting what is there, just don't overwrite anything :)

The correct place for altering links is generally hook_node_view_alter(), as you mentioned.

For adding your own links it is hook_node_view()

As an example see http://drupal.org/node/224333#node_links