Regarding Spotlight, one thing that started happening for me on Sequioa was that Finder and other apps started getting very slow to react to file changes. For example, I can save a new file to a directory, and the Finder window takes maybe 10-20 seconds before the file shows up in the list. If I navigate to a different folder and then back, the file is there. I notice the same delay in apps like IntelliJ.
I could be wrong, but apparently Spotlight is the service that drives this kind of file system watching. I think macOS has a lower-level inotify-style file system event API, which should be unaffected, but Finder and these other apps apparently use Spotlight. I really wish I had a fix, because it's just crazy having to constantly "refresh" things.