Currently your choices are emacs/vim over SSH or sync from your local machine (where the code intelligence / debugging integration probably doesn't work as desired).
A web IDE allows an arbitrarily powerful cloud instance to do the heavy lifting of build/test/code intelligence while the developer still gets a full-featured GUI IDE. Especially since VS Code and Atom are Electron apps, it's a natural step to use them to edit remote files. Better than VNC, anyway.
VNC isn't the right way to go in these cases. If a company is asking its developers to do remote work over VNC, and they aren't a three-person company struggling with financial and administrative resources, what they need is an IT manager and/or a build system engineer, not a web IDE. We already have plenty of IDEs that can't hold a candle to Visual Studio, the umpteenth one BUT ON THE WEB is pretty much the last thing we need.