I agree with you on principle but disagree on the context of the question. What the other poster is asking is if you want to obscure something behind JavaScript that is critical to the use of your website, and the answer should be "no."
You shouldn't make essential parts and behavior of your application/website reliant on client side javascript, and in this context, the person asking the original question would be having a website without navigation for someone without JS. If he's going to create a fallback for it, then he may as well just not use JS to load the navigation because the time it takes to maintain the fall back is the same time it takes to just do it right without relying on JS in the first place.
For some legit (but annoying) reasons, we get millions of visits a year from people who disable JavaScript. More visitors have disabled JS than we have IE10 (and older) users, which is a striking percentage. There's surprisingly a good reason for many of them that answer our surveys/interviews, they work for government, science, and research industries where they have to disable JS on their primary work station for security reasons, but need our software documentation (I work for a company that makes a popular programming language for engineers and scientists). If you go to our website, it renders horribly without JavaScript, just looks like complete shit, but everything is still there for somebody to get around for the most part. THere's almost no core functionality of the basic, navigable website that doesn't work without JavaScript.
Making a critical component not render if the client doesn't have JS is bad practice, even if your'e of the "c'mon bro" audience which I generally am. It's one thing to have image sliders, off canvas nav, text bubbles, auto-complete, and other extra features not work, but to have your primary nav not even render in the dom shouldn't be a consideration. In this case, there is virtually no benefit to putting your navigation behind a JavaScript fence, and only drawbacks... Creating a fallback in this case would take the same amount of time to just doing it the right way.