Those animations are absolutely a product of well researched UX design, it's just design that's intended to make the UI more accessible by showing users the flow of information and how the structure of the interface changes in a visual manner, rather then design intended to address the needs of power users. The animations used in the Spaces feature on MacOS is a good example of that, where apps and desktops slide and zoom around to make it absolutely obvious that the apps you have open haven't just disappeared. That's quite important for a fairly advanced desktop manipulation feature like that.
Modern operating systems are designed for broad audiences, and that includes people who aren't as savvy with technology as we are. That means accepting some level of tradeoffs between the speed that pro users want, and UI accessibility that necessitates slowing things down somewhat. In the case of desktop OS's there's still usually ways for power users to disable that stuff and of course Terminal for those who don't really need a UI at all. And then there's a lot of different flavors of Linux that make no attempt at appealing to a less technical audience.
But just because you're not the target audience doesn't mean the UX team are "idiots" or that the companies are "stupid". The amount of novice or casual users is orders of magnitude higher then power users who care only about efficiency, and for better or worse those users always come first.
Locating the window I'm looking for takes longer than the animation and I can start looking immediately during the fade. Even with the ctrl+number shortcuts, I can't get my hands back onto the home row before the animation finishes.