One of the commonly touted maxims regarding responsive web design is: if you don't have something on the screen at smaller viewports, you shouldn't have it there at larger ones either.
This means users should be able to accomplish all the same goals (buy a product, read an article, accomplish an interface task) at every viewport size. This is common sense. After all, as users ourselves, we've all felt the frustration of going to a website to accomplish a goal and being unable to, simply because we're using a smaller screen.
It also means that as screen real estate is more plentiful, we shouldn't feel compelled to add extra things just to fill the space (widgets, adverts, or links for example). If the user could live without those extras at smaller screen sizes, they'll manage just fine at bigger ones. Displaying extra content at larger viewport sizes also means that either the content was there at smaller viewports and was merely hidden (typically using display: none; in CSS) or it's being loaded in at a particular viewport size (with the help of JavaScript). Succinctly: either the content is loaded but not viewable, or it's viewable yet probably superfluous.
In broad terms I think the above maxim is sound advice. If nothing else, it makes designers and developers question more thoroughly the content they display on screen. However, as ever in web design, there are always going to be exceptions.
As far as possible, I resist loading in new markup for different viewports but occasionally it's a necessity. I've worked on complex user interfaces that rightfully required different markup and designs at wider viewports.
In this instance, JavaScript was used to replace one area of markup with another. It wasn't the ideal scenario but it was the most pragmatic. If, for whatever reason, the JavaScript failed, users got the smallest screen layout. They could accomplish all the same goals, just the layout was sub-optimal for achieving the task at hand.
These are the kind of choices you will likely face as you code more and more complex responsive web designs, and you'll need to use your own judgment as to what the best choice is in any given scenario. However, it's not a cardinal sin if you toggle the visibility of the odd bit of markup with display: none to achieve your goal.
It's a fact that JavaScript provides a level of interactivity on webpages that simply cannot be achieved with CSS alone. However, where possible, when it comes to visuals, we should still do all the heavy lifting with CSS. In practicality, this means not animating menus in, out, on and off, with JavaScript alone (I'm looking at you jQuery show and hide methods). Instead, use JavaScript to perform simple class changes on the relevant section of the markup. Then let that class change trigger the menu being shown/animated in CSS.
For the best performance, when toggling classes in the HTML, ensure you add a class as close as possible to the item you want to effect. For example, if you want a pop-up box to appear over another element, add the class on the closest shared parent element. This will ensure that, for the sake of optimal performance, only that particular section of the page is made 'dirty' and the browser shouldn't have to paint vast areas of the page again. For a great, free, course on performance, take a look at Paul Lewis's 'Browser Rendering Optimization' course: https://www.udacity.com/course/browser-rendering-optimization--ud860