Sometimes I have some unsaved work (like a text file opened in Kate) when trying to logout/shutdown, although plasma will warn me about any unsaved work, latte dock exits immediately, regardless of whether logout/shutdown is interrupted. I suggest that latte dock exits only when plasmashell exits during a logout/shutdown process.
the thing is that it doesnt exit... for some reason plasma/kwin decides that it should make them invisible... if you try Multiple layouts you will notice that panels become invisible and visible afterwards (that is a Latte workaround that I could enable also for Single mode but I would prefer plasma/kwin devs opinion first)
*** This bug has been marked as a duplicate of bug 397858 ***
Alright, at least I know where the problem is. Made a temporary fix : https://gist.github.com/maz-1/f6941f4cf22b9c95dd3b1e419809f99e