The train ferry to Sicily (Villa San Giovanni-Messina) is still there and in full use - I used it in October.
Trenitalia has tried to close the service several times, but it's still there...
There is a proposed road/rail bridge project over the 2-mile strait, but it keeps getting cancelled for both economic and environmental reasons.
Being in an active earthquake area doesn't help, and the locals want to retain the port/railway jobs.
So there's no risk to the train ferry for the immediate future.
It takes the best part of 2 hours from arrival at one side, splitting and shunting the portions on board, a 20-minute crossing and shunting off on the other side.
You can stay on the train, or take a stroll on the ferry.
It also keeps traditional LHCS on the main trains to Sicily.
https://en.wikipedia.org/wiki/Strait_of_Messina_Bridge
The Fehmarn Belt tunnel replacing the Puttgarden-Rødby train ferry is in planning, with consultancy contracts let and completion planned for 2028.
The main obstacle is German approval (funding and environmental).
The railway on both sides will also be upgraded.
Currently the DMU trains roll directly on/off the ferry without shunting, but you have to leave the train while on board.
Very efficient (compared to the Messina crossing), and takes about an hour all told.
https://en.wikipedia.org/wiki/Fehmarn_Belt_Fixed_Link
http://www.railwaygazette.com/news/...s-signed.html?sword_list[]=fehmarn&no_cache=1