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.
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)
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.
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.
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).
One approach is to build a hierarchy