Not necessarily. Nav inside article functions the same as the contents list in a Wikipedia article so if you don't want that, you can remove it from the article. If you want secondary links to other related content, those should go in a different nav in aside. If you want site-wide links, you can create a separate nav outside the article.
Also of note, footer can be for the article or the whole page. If you like, you can put footer outside the article and put the site-wide navigation there in addition to any forms.
Skip to content links aren't hacks, but are in fact part of standard procedure for web accessibility and do solve a problem with fewer steps. Try not to look at things that don't necessarily conform to arbitrary standards of elegance as hacks.