Removing big nav bars and moving their contents into drop-down menus is pretty much the standard way of handling resizes across the web. Same goes for multi-column layouts. It would be a horrible idea to keep those things on a phone, just like it's a horrible idea to scale up a phone interface to a desktop browser window.
Having distinct layouts for mobile devices can be a good idea.
Having the interface add/remove elements for this dynamically is (a) obviously not necessary, as my desktop doesn't suddenly turn into a phone while I am browsing, and (b) not a good idea.
It seems like a neat generalisation, but it really isn't.
Just to point out why your statement is misinformed, your tablet turns from a desktop to a phone when you rotate it.
I've been designing web frameworks from the ground up since 1995. Two sizes is not how it works. You don't read the initial size of the browser window, or parse the device data to see if it's mobile, and decide from there which of two layouts to draw (mobile or desktop). You read it on the fly and redraw as necessary. All parts of the interface and the content working together.
Bootstrap, for instance, has xs, sm md lg xl classes and mixins. Often you don't hide interface elements but simply resize them. Font leading and size may change 20 times subtly as you resize a window.
If you don't believe me, load any major website in a desktop browser and play with resizing the window from narrow to wide.
If done wrong, it's bad because you're on a desktop and seeing a mobile interface when you shouldn't. The Charles Schwab website is an example of that. If done right, it should feel natural on any size screen, and you should have visual cues as you resize. Again, in many cases it's not about hiding UI elements completely, but about simplifying them so they degrade from word+icon, to smaller font, to just icon, to drop menu. Although it's hardly an example of cutting edge design, the overall AWS console handles this pretty well, shuffling what you need into smaller compartments. (Some individual services do better than others). If you open 4 of them on a desktop it's still fairly easy to find what you need, and hasn't yet degraded all the way to a mobile interface. In my app designs there are at least three levels, usually four.
The main reason you don't recall apps doing that is that it is a pretty horrible idea in virtually all cases.