I keep reading these articles about how awful hamburgers are but so far not a single one addresses menus that have more than 3-5 items. I manage sites that we have kicked around ideas for how to deal with the menu better, but the size of what is in that menu makes all the proposed ideas I've seen not feasible. So I'm right there with you that it is unfortunate, I wish these articles had more in way of solutions than just regurgitating what we've heard for a while, hamburgers suck.
Somewhere along the way I realized that design skill has as much to do with making convincing business cases for simplifying your business offering as it does with what design patterns we use. Approached this way, these types of articles help in the same way software design patterns do: perhaps refactoring the code will improve the smell, but its also possible we have an unnecessarily complex business problem ("50 more news categories than anyone will ever actually browse through", for example), and we need to make a case for simplifying the architecture.
This is an important point. You contribute most as a designer when you control or influence whatever is necessary to get to good design. In most cases, the largest levers of influence are not in which design patterns you use, but in the business decisions that make things simple or complex.
In retrospect, I should have clarified what I meant by recommending the 3- to 5-item menu in the article; I was assuming the need to consolidate the menu to that many items on mobile, even if it wasn't so consolidated on larger views. There many need to be a "junk drawer" as others here have mentioned, or maybe those secondary items rely on navigation in the content itself.
I think the best practice might be to pare down the navigation to the most important items, so at least those have visibility in a mobile context. However, these are still new design patterns being established, so nobody really has solid answers yet.
I'm gonna sound like an old fart now (mostly because I am) but back in the late 90s we used to have a discipline called Information Architecture that existed to handle exactly this case.
You see, Information Architecture has more to do with capital D Design, not fad, bandwagons and styles. Its about solving this exact problem. I really hope the concept of User Experience dies in a fire so we can go back to real Design.
(User Experience is in my opinion the most nebulous, snake-oil concept I've heard since SEO. Users don't want "an experience". They want to get in get what they want and to get out. The experience should be invisible)
Perhaps the term IxD (Interaction Design) would sit better with you than UX. IxD includes UX but also Info Architecture and has a lot more to do with structuring information before any 'design' takes place. In IxD you wouldn't normally touch on users or appearance (affordances for example is far off down the road at this point) before you sort out the "what is it?" and "what data?". It's very easy to start thinking about the users, too easy in fact, that many self-proclaimed 'UX-experts' focus on that and forget that 'content is still king' and it's presentation may actually attract users, so don't try to tailor shit to maggots when you can create a garden and attract bees.
I'm not so sure UX can be dismissed that easily. IA deals with content hierarchies rather than things like "navigation efficiency" details or site registration journeys, or touch interaction behaviours and optimisation.
There's cross-over, but one "Designer" can't do it all, even if they have a good grasp of everything.
When the focus is on UX, decisions might be made about how people sign in or out. The UX expert might determine that a 2-step log out process is one step too many, but the research they gather might suggest it's nevertheless still acceptable enough to get away with. The designer makes whatever-step process look and function the best it can, without needing to scrutinise the research and testing around 2-step sign out processes.
Another example - consider the user experience of dismissing the banner that appears on some websites that have an app in iOS Safari. The little 'X' close link is tiny, way smaller than any touch button or link should be. Bad UX? Sure is. But the UX person must have data suggesting that having a stupidly small close button for that banner is worth it for the primary visual incentive to act on the promotional prompt without annoying too many people (annoys the hell out of me, but I'm not everyone).
OK, so what does IA have to say about this problem? From what I remember about it (my course didn't have it, but I read a bunch in the early 2000s), it was more concerned about the overall organization of the information over the pages, and not with the specifics of how a menu should be formatted.
By the way, it's not "an" experience, it's "the" experience, and nobody would agree more with you about it being invisible than the coiner of the term UX - after all, Don Norman's seminal work (The Design of Everyday Things) was all about designing stuff to be more intuitive and fast to use.
You can redef UX to mean something bad, but it's obvious that it is supposed to be UI + how stuff works instead of just the graphical part. Also, X's are sexy. Even that big rocket company decided to just take Space and put an X on it.
SEO might have plenty of snake oil vendors, but it is, unfortunately, a very real and immensely lucrative thing. Search engines drive traffic, which drives money. Search engines are gameable. End of story.