Yeah, that is what I did:
cp ~/.config/plasma-org.kde.plasma.desktop-appletsrc ~/.config/plasma-org.kde.plasma.desktop-appletsrc.bak
rm ~/.config/plasma-org.kde.plasma.desktop-appletsrc && qdbus org.kde.ksmserver /KSMServer logout 0 3 3
Session relogged and it gave me black screen (no wallpaper) and default Plasma panel at the bottom. However, this didn't fix the issue. Both, the systray on latte and on default's panel is missing elements.
I restored my previous config.
My test user doesn't have this problem, so this is happening for personalized systray and the issue is within configs. Which one? Hmm... I submitted a bug and hope that someone will reveal more about it.