It is more code efficient to modify the actual template (or code) than to use a plugin. However, sometimes it is easier when upgrading to have all the modifications in a plugin. I think it really depends on the site. I know I have several plugins, but I would rather modify my navbar template than use a plugin for it. I have removed several of the default vbulletin navbar links, so since I have to modify the navbar template anyway, I might as well just add my links in the template.
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