could i overwrite the array value by the preprocess function?
You could only overwrite them if they are accessible within template_preprocess_node(). For example, if the module adds $links to the $vars (or $variables) array, or to the $node object, in its own implementation of preprocess_node(), you could simply do:
$vars['links'][0]['text'] = "i have changed this text";
If the module does not add $links to the $vars/$variables array or to the node object, you would not be able to change it from mytheme_preprocess_node().