Basically what happeded to me is described here: OSMC Skin Bug - "Show empty TV shows" disabled setting ignored upon initial node entry - #12 by Alamei
The link for the TV Shows menu item was not set to Common > TV Shows (via the link videodb://movies/titles/) when I had the issue but rather some other node was selected (cannot remember now, maybe Videos > TV Shows > Titles, the link was library://video/movies/titles.xml/).
I originally had v16 Kodi which was updated to v17 then v18, maybe the v16 version still had the old link which was carried over to v17+18 or maybe I manually changed it sometime (can’t recall it).