> Since when? What have they been replaced with?

The Helsingborg-Helsingør train ferry was replaced (car ferries remain) by railway on the Öresund Bridge (from the 2011 TV series The Bridge) between the big cities Malmö, Sweden and Copenhagen, Denmark in 2000. https://en.wikipedia.org/wiki/%C3%98resund_Bridge

The Puttgarden-Rødby train ferry was replaced by a new longer but faster railway route via the Great Belt Bridge and Flensburg until the Fehmarn Belt Fixed Link is ready. https://www.seat61.com/trains-and-routes/hamburg-to-copenhag...