I managed to narrow it down to Cinesamples CinePiano. If that Kontakt instrument is playing, Popping is present on stop. If I don't have it in my arrangement, there's no popping whatsoever. Something's fishy there. Might still be a Kontakt bug because I use CinePiano for years and recently updated Kontakt and don't recall having this issue prior to that so I'll give Cinesamples the benefit of the doubt, but I'll try to investigate more.
Long story short, check your plug-ins and instruments if you're having this popping issue, might not even be your hardware/Logic.