I am curious why that happens. From some Googling it seems like the updater copies itself to a random directory each time it runs [1], and I guess Little Snitch classifies programs by their full path, so it sees it as a new program each time.

Copying itself is odd and probably suboptimal behavior, but it is explainable without assuming malice: my guess is that it’s related to some kind of “before we update let’s update the updater” bootstrapping logic. I could be wrong, but IIRC the updater code is open source, so it should be easy to find out.

[Edit: Oops, it's actually not open source. Their Windows updater (Omaha) is open source, but their Mac one (Keystone) is not. Of course, one can still open the binaries in a decompiler.]

Regardless, moving a program around on disk, or even deleting the program while it’s running (which is possible on macOS), would not prevent it from showing up in Activity Monitor.

[1] http://www.reecefowell.com/2012/11/16/ksfetch-annoyance-on-m...