I use hotkeys for filters, yes. If I had to access the menus every time I wanted to hide/unhide things I'd go insane. I wouldn't toggle them on/off nearly as much as I do, and my workflow would be slower and more limited.
As an example, I very often toggle visportals on/off for adjustments, or func_statics for inspecting world geometry.
And sometimes I have to turn off all filters so that I'm 100% sure I'm copying or moving geometry properly, without leaving behind hidden clips, triggers, visportals, nodraws, etc.
And then I have to re-hide all the things I like to keep hidden. I don't know about your workflow, but 99% of the time, I keep collisions, shadows, sky, visportals, triggers, nodraws, and also caulks, all hidden and out of my way. With hotkeys I just press alt and a bunch of keys in succession, and it takes me seconds. With menus it would take a while.
There's no way I could ever not use hotkeys. I'd go completely nuts.
No, I'm saying they require more work than just simply creating a layer and putting stuff in it. And if you don't put a hotkey on it, it's also more work to use.
I'm not saying you can't use them for that. I'm saying they're not the right tool for it.
EDIT: Keep in mind that the example above is just one example. There's all sorts of things you might want to use that functionality I suggested for. And again, layers are map-specific. If you setup filters for layers (is that even really possible?), then your filters menu will grow, and become polluted with junk that only works on certain maps. And the more you do it, the worse it gets.
Back when I could used that in Hammer, I always had quite a few layers per map that controlled visibility of specific groups of objects. When you can just go wild with it, you go wild with it.