Hook-Handed Man says he liked the theatre troupe better before Yoko arrived. That's a reference to a popular belief that John Lennon marrying Yoko Ono caused The Beatles to break up.
In the Library of Records, Violet and Klaus pass a file labeled "Slippery Slopes." This is a reference to the tenth book in A Series of Unfortunate Events, "The Slippery Slope."
When the siblings are scrolling through the filing cabinet in the hospital, the last file is labeled "sniffer, cake" a reference to the term used by Carmalita Spats in The Austere Academy: Part One (2018).
Count Olaf (NPH) continues the long running gag of breaking the fourth wall when he's sat watching the CCTV monitors in the HR/Admin office, saying "I hate boring television" before looking directly into the camera lens for a couple of seconds.
When Olaf makes his grand entrance at Last Chance General Store, he strokes one of the white, porcelain cat figures. Male villains stroking a white cat is a common trope in fiction.